BCOeditor Wiki - User contributions [en]

BCO Pilot Project

2024-05-20T17:28:59Z

ChinweokeO: /* Estimated Collaborations */

== Pilot Project ==
BioCompute is shorthand for IEEE 2791-2020, a [https://standards.ieee.org/ieee/2791/7337/ standard for communicating computational workflows]. The standard was developed in response to difficulties in recording and interpreting bioinformatics pipelines. BioCompute is a framework for step by step description of computational workflows. BioCompute defines what content must be included, and what form it should take. It includes data provenance and rich metadata to eliminate ambiguity. The standard also includes an “Execution Domain” for re-executing a pipeline, if desired.

Three Centers at the FDA [https://www.federalregister.gov/documents/2020/07/22/2020-15771/electronic-submissions-data-standards-support-for-the-international-institute-of-electrical-and have adopted the standard] (see notice in Federal Registry by the Food and Drug Administration on 07/22/2020) for bioinformatics applications. To increase adoption of BioCompute and bring awareness within and outside of FDA we propose a pilot with the BioCompute team, FDA and industry. Because the standard was developed to manage complexity and reduce the organizational burden on FDA reviewers and regulated industry submitting to them, the purpose of this pilot project is to bring both sides in agreement around its usage thereby streamlining and standardizing computational workflow submissions and reviews. Participating sponsors will prepare and submit a computational workflow with a BioCompute Object (BCO) without any additional clarification, and FDA reviewers will review the BCO. Initial planning meetings, gathering project materials, preparing and submitting BCOs, BCO review, and final debrief are expected to take one year.

== Expected Outcome ==

=== Documentation and Reporting ===
Throughout the process, we will document anything that is difficult to understand, barriers to working with or reading the BCO, and any other general issues. As a result, a [https://wiki.biocomputeobject.org/Best_Practices best practices document] and [https://wiki.biocomputeobject.org/Security_Plan security plan] have been generated to support the standard and there may be additional training materials, created as needed to enable a group to prepare or read a BCO with minimal training. These resources are meant to support the standard as a vehicle for more fluid communication, and to enable a group to prepare or read a BCO with minimal training.

In addition, groups that participate in the pilot will have first-hand knowledge of submitting computational analyses and how to do so efficiently. Monthly reports are also submitted to maintain communication of plans and processes as they occur.

== Request ==

=== Collaboration and Communication ===
To have the most impact, this project requires input from multiple groups with close collaboration with FDA-HIVE team. We’re asking FDA reviewers who review any work that contains a computational pipeline to participate. Examples of computational pipelines include a medical device for the detection of physiological warning signs, a diagnostic test for the presence of pathogenic species, supporting evidence for a new drug application in the form of NGS analyses, or others.

Only the computational portion need be submitted, and participants will use their own data for submission. Data submitted need not be actual clinical data, however, the more similar the data to a real submission, the more valuable the pilot. Participating FDA reviewers will be asked to review the pilot submission with no additional input, and to document anything they feel is unclear or not presented well.

Participating sponsors are asked to prepare realistic regulatory submissions using one or more BCOs to describe their work. We estimate that the project will require some level of effort from all participants. The representative(s) will be involved in planning, gathering the materials for submission, and learn how to represent their data in the BCO, as well as meetings and documentation for the pilot project.

Groups are asked to meet with us to explain difficulties working with the standard. Groups may decide to meet with us individually, if they desire, rather than as part of a larger meeting with the other groups.

=== Estimated Contributions ===
{| class="wikitable"
!'''Organization'''

'''Platform'''
!'''Personnel'''
!'''FTE'''
!'''Months'''
!'''Tasks'''
|-
|Velsera BCO platform
|Coordinator
|0.5
|12
|Project Liaison with technical team, platform representative
|-
|DNAnexus BCO platform
|Coordinator
|0.5
|12
|Project Liaison with technical team, platform representative
|-
|FDA-HIVE BCO platform
|Reviewer/Technologist
|1.5
|12
|Review submissions, document feedback, update HIVE
|-
|George Washington BCOdb and BCO-form
|Project Manager+Technical Lead for BCOdb and form-based submission)
|1
|12
|Overall plan, organize regular meetings/agendas/schedules, project documentation
|-
|Industry Participants (3 total; will be paired with GW, SBG and DNAnexus)
|Coordinator
|0.5/participant
|12
|Gather materials, coordinate pilot submission internally
|-
|FDA
|Lead Reviewer
|As needed
|
|
|}

=== Challenges and Solutions ===
During development and maintenance of the platform, users may run into bugs and may have suggestions regarding the user interface (UI). To address these challenges, users can submit their feedback and report issues via the website's [https://github.com/biocompute-objects/portal_userdb/issues/new/choose 'Report an Issue'] link. This feedback is useful in refining the platform and enhancing the overall user experience. Additionally, to ensure continuous effectiveness and functionality of BioCompute Objects (BCOs), regular updates and enhancements are made based on testing and user feedback.

== References and Resources ==
For additional information, please refer to the resources below:

* [https://wiki.biocomputeobject.org/index.php?title=Main_Page BioCompute Objects Wiki]
* [https://wiki.biocomputeobject.org/White_paper White Paper]

=== Contact ===
For any questions or to participate in the pilot, please email Jonathon Keeney, project co-PI at George Washington University: keeneyjg@gwu.edu

BCO Pilot Project

2024-05-20T17:28:31Z

ChinweokeO: /* Request */

== Pilot Project ==
BioCompute is shorthand for IEEE 2791-2020, a [https://standards.ieee.org/ieee/2791/7337/ standard for communicating computational workflows]. The standard was developed in response to difficulties in recording and interpreting bioinformatics pipelines. BioCompute is a framework for step by step description of computational workflows. BioCompute defines what content must be included, and what form it should take. It includes data provenance and rich metadata to eliminate ambiguity. The standard also includes an “Execution Domain” for re-executing a pipeline, if desired.

Three Centers at the FDA [https://www.federalregister.gov/documents/2020/07/22/2020-15771/electronic-submissions-data-standards-support-for-the-international-institute-of-electrical-and have adopted the standard] (see notice in Federal Registry by the Food and Drug Administration on 07/22/2020) for bioinformatics applications. To increase adoption of BioCompute and bring awareness within and outside of FDA we propose a pilot with the BioCompute team, FDA and industry. Because the standard was developed to manage complexity and reduce the organizational burden on FDA reviewers and regulated industry submitting to them, the purpose of this pilot project is to bring both sides in agreement around its usage thereby streamlining and standardizing computational workflow submissions and reviews. Participating sponsors will prepare and submit a computational workflow with a BioCompute Object (BCO) without any additional clarification, and FDA reviewers will review the BCO. Initial planning meetings, gathering project materials, preparing and submitting BCOs, BCO review, and final debrief are expected to take one year.

== Expected Outcome ==

=== Documentation and Reporting ===
Throughout the process, we will document anything that is difficult to understand, barriers to working with or reading the BCO, and any other general issues. As a result, a [https://wiki.biocomputeobject.org/Best_Practices best practices document] and [https://wiki.biocomputeobject.org/Security_Plan security plan] have been generated to support the standard and there may be additional training materials, created as needed to enable a group to prepare or read a BCO with minimal training. These resources are meant to support the standard as a vehicle for more fluid communication, and to enable a group to prepare or read a BCO with minimal training.

In addition, groups that participate in the pilot will have first-hand knowledge of submitting computational analyses and how to do so efficiently. Monthly reports are also submitted to maintain communication of plans and processes as they occur.

== Request ==

=== Collaboration and Communication ===
To have the most impact, this project requires input from multiple groups with close collaboration with FDA-HIVE team. We’re asking FDA reviewers who review any work that contains a computational pipeline to participate. Examples of computational pipelines include a medical device for the detection of physiological warning signs, a diagnostic test for the presence of pathogenic species, supporting evidence for a new drug application in the form of NGS analyses, or others.

Only the computational portion need be submitted, and participants will use their own data for submission. Data submitted need not be actual clinical data, however, the more similar the data to a real submission, the more valuable the pilot. Participating FDA reviewers will be asked to review the pilot submission with no additional input, and to document anything they feel is unclear or not presented well.

Participating sponsors are asked to prepare realistic regulatory submissions using one or more BCOs to describe their work. We estimate that the project will require some level of effort from all participants. The representative(s) will be involved in planning, gathering the materials for submission, and learn how to represent their data in the BCO, as well as meetings and documentation for the pilot project.

Groups are asked to meet with us to explain difficulties working with the standard. Groups may decide to meet with us individually, if they desire, rather than as part of a larger meeting with the other groups.

=== Estimated Collaborations ===
{| class="wikitable"
!'''Organization'''

'''Platform'''
!'''Personnel'''
!'''FTE'''
!'''Months'''
!'''Tasks'''
|-
|Velsera BCO platform
|Coordinator
|0.5
|12
|Project Liaison with technical team, platform representative
|-
|DNAnexus BCO platform
|Coordinator
|0.5
|12
|Project Liaison with technical team, platform representative
|-
|FDA-HIVE BCO platform
|Reviewer/Technologist
|1.5
|12
|Review submissions, document feedback, update HIVE
|-
|George Washington BCOdb and BCO-form
|Project Manager+Technical Lead for BCOdb and form-based submission)
|1
|12
|Overall plan, organize regular meetings/agendas/schedules, project documentation
|-
|Industry Participants (3 total; will be paired with GW, SBG and DNAnexus)
|Coordinator
|0.5/participant
|12
|Gather materials, coordinate pilot submission internally
|-
|FDA
|Lead Reviewer
|As needed
|
|
|}

=== Challenges and Solutions ===
During development and maintenance of the platform, users may run into bugs and may have suggestions regarding the user interface (UI). To address these challenges, users can submit their feedback and report issues via the website's [https://github.com/biocompute-objects/portal_userdb/issues/new/choose 'Report an Issue'] link. This feedback is useful in refining the platform and enhancing the overall user experience. Additionally, to ensure continuous effectiveness and functionality of BioCompute Objects (BCOs), regular updates and enhancements are made based on testing and user feedback.

== References and Resources ==
For additional information, please refer to the resources below:

* [https://wiki.biocomputeobject.org/index.php?title=Main_Page BioCompute Objects Wiki]
* [https://wiki.biocomputeobject.org/White_paper White Paper]

=== Contact ===
For any questions or to participate in the pilot, please email Jonathon Keeney, project co-PI at George Washington University: keeneyjg@gwu.edu

BCO Pilot Project

2024-05-20T17:27:54Z

ChinweokeO: /* Expected Outcome */

== Pilot Project ==
BioCompute is shorthand for IEEE 2791-2020, a [https://standards.ieee.org/ieee/2791/7337/ standard for communicating computational workflows]. The standard was developed in response to difficulties in recording and interpreting bioinformatics pipelines. BioCompute is a framework for step by step description of computational workflows. BioCompute defines what content must be included, and what form it should take. It includes data provenance and rich metadata to eliminate ambiguity. The standard also includes an “Execution Domain” for re-executing a pipeline, if desired.

Three Centers at the FDA [https://www.federalregister.gov/documents/2020/07/22/2020-15771/electronic-submissions-data-standards-support-for-the-international-institute-of-electrical-and have adopted the standard] (see notice in Federal Registry by the Food and Drug Administration on 07/22/2020) for bioinformatics applications. To increase adoption of BioCompute and bring awareness within and outside of FDA we propose a pilot with the BioCompute team, FDA and industry. Because the standard was developed to manage complexity and reduce the organizational burden on FDA reviewers and regulated industry submitting to them, the purpose of this pilot project is to bring both sides in agreement around its usage thereby streamlining and standardizing computational workflow submissions and reviews. Participating sponsors will prepare and submit a computational workflow with a BioCompute Object (BCO) without any additional clarification, and FDA reviewers will review the BCO. Initial planning meetings, gathering project materials, preparing and submitting BCOs, BCO review, and final debrief are expected to take one year.

== Expected Outcome ==

=== Documentation and Reporting ===
Throughout the process, we will document anything that is difficult to understand, barriers to working with or reading the BCO, and any other general issues. As a result, a [https://wiki.biocomputeobject.org/Best_Practices best practices document] and [https://wiki.biocomputeobject.org/Security_Plan security plan] have been generated to support the standard and there may be additional training materials, created as needed to enable a group to prepare or read a BCO with minimal training. These resources are meant to support the standard as a vehicle for more fluid communication, and to enable a group to prepare or read a BCO with minimal training.

In addition, groups that participate in the pilot will have first-hand knowledge of submitting computational analyses and how to do so efficiently. Monthly reports are also submitted to maintain communication of plans and processes as they occur.

== Request ==

=== Collaboration and Communication ===
To have the most impact, this project requires input from multiple groups with close collaboration with FDA-HIVE team. We’re asking FDA reviewers who review any work that contains a computational pipeline to participate. Examples of computational pipelines include a medical device for the detection of physiological warning signs, a diagnostic test for the presence of pathogenic species, supporting evidence for a new drug application in the form of NGS analyses, or others.

Only the computational portion need be submitted, and participants will use their own data for submission. Data submitted need not be actual clinical data, however, the more similar the data to a real submission, the more valuable the pilot. Participating FDA reviewers will be asked to review the pilot submission with no additional input, and to document anything they feel is unclear or not presented well.

Participating sponsors are asked to prepare realistic regulatory submissions using one or more BCOs to describe their work. We estimate that the project will require some level of effort from all participants. The representative(s) will be involved in planning, gathering the materials for submission, and learn how to represent their data in the BCO, as well as meetings and documentation for the pilot project.

Groups are asked to meet with us to explain difficulties working with the standard. Groups may decide to meet with us individually, if they desire, rather than as part of a larger meeting with the other groups.

{| class="wikitable"
!'''Organization'''

'''Platform'''
!'''Personnel'''
!'''FTE'''
!'''Months'''
!'''Tasks'''
|-
|Velsera BCO platform
|Coordinator
|0.5
|12
|Project Liaison with technical team, platform representative
|-
|DNAnexus BCO platform
|Coordinator
|0.5
|12
|Project Liaison with technical team, platform representative
|-
|FDA-HIVE BCO platform
|Reviewer/Technologist
|1.5
|12
|Review submissions, document feedback, update HIVE
|-
|George Washington BCOdb and BCO-form
|Project Manager+Technical Lead for BCOdb and form-based submission)
|1
|12
|Overall plan, organize regular meetings/agendas/schedules, project documentation
|-
|Industry Participants (3 total; will be paired with GW, SBG and DNAnexus)
|Coordinator
|0.5/participant
|12
|Gather materials, coordinate pilot submission internally
|-
|FDA
|Lead Reviewer
|As needed
|
|
|}

=== Challenges and Solutions ===
During development and maintenance of the platform, users may run into bugs and may have suggestions regarding the user interface (UI). To address these challenges, users can submit their feedback and report issues via the website's [https://github.com/biocompute-objects/portal_userdb/issues/new/choose 'Report an Issue'] link. This feedback is useful in refining the platform and enhancing the overall user experience. Additionally, to ensure continuous effectiveness and functionality of BioCompute Objects (BCOs), regular updates and enhancements are made based on testing and user feedback.

== References and Resources ==
For additional information, please refer to the resources below:

* [https://wiki.biocomputeobject.org/index.php?title=Main_Page BioCompute Objects Wiki]
* [https://wiki.biocomputeobject.org/White_paper White Paper]

=== Contact ===
For any questions or to participate in the pilot, please email Jonathon Keeney, project co-PI at George Washington University: keeneyjg@gwu.edu

BCO Pilot Project

2024-05-20T17:07:47Z

ChinweokeO: /* Challenges and Solutions */

== Pilot Project ==
BioCompute is shorthand for IEEE 2791-2020, a [https://standards.ieee.org/ieee/2791/7337/ standard for communicating computational workflows]. The standard was developed in response to difficulties in recording and interpreting bioinformatics pipelines. BioCompute is a framework for step by step description of computational workflows. BioCompute defines what content must be included, and what form it should take. It includes data provenance and rich metadata to eliminate ambiguity. The standard also includes an “Execution Domain” for re-executing a pipeline, if desired.

Three Centers at the FDA [https://www.federalregister.gov/documents/2020/07/22/2020-15771/electronic-submissions-data-standards-support-for-the-international-institute-of-electrical-and have adopted the standard] (see notice in Federal Registry by the Food and Drug Administration on 07/22/2020) for bioinformatics applications. To increase adoption of BioCompute and bring awareness within and outside of FDA we propose a pilot with the BioCompute team, FDA and industry. Because the standard was developed to manage complexity and reduce the organizational burden on FDA reviewers and regulated industry submitting to them, the purpose of this pilot project is to bring both sides in agreement around its usage thereby streamlining and standardizing computational workflow submissions and reviews. Participating sponsors will prepare and submit a computational workflow with a BioCompute Object (BCO) without any additional clarification, and FDA reviewers will review the BCO. Initial planning meetings, gathering project materials, preparing and submitting BCOs, BCO review, and final debrief are expected to take one year.

== Expected Outcome ==

=== Documentation and Reporting ===
Throughout the process, we will document anything that is difficult to understand, barriers to working with or reading the BCO, and any other general issues. As a result, a [https://wiki.biocomputeobject.org/Best_Practices best practices document] and [https://wiki.biocomputeobject.org/Security_Plan security plan] have been generated to support the standard and there may be additional training materials, created as needed to enable a group to prepare or read a BCO with minimal training. These resources are meant to support the standard as a vehicle for more fluid communication, and to enable a group to prepare or read a BCO with minimal training.

In addition, groups that participate in the pilot will have first-hand knowledge of submitting computational analyses and how to do so efficiently. Monthly reports are also submitted to maintain communication of plans and processes as they occur.

== Request ==

=== Collaboration and Communication ===
To have the most impact, this project requires input from multiple groups with close collaboration with FDA-HIVE team. We’re asking FDA reviewers who review any work that contains a computational pipeline to participate. Examples of computational pipelines include a medical device for the detection of physiological warning signs, a diagnostic test for the presence of pathogenic species, supporting evidence for a new drug application in the form of NGS analyses, or others.

Only the computational portion need be submitted, and participants will use their own data for submission. Data submitted need not be actual clinical data, however, the more similar the data to a real submission, the more valuable the pilot. Participating FDA reviewers will be asked to review the pilot submission with no additional input, and to document anything they feel is unclear or not presented well.

Participating sponsors are asked to prepare realistic regulatory submissions using one or more BCOs to describe their work. We estimate that the project will require some level of effort from all participants. The representative(s) will be involved in planning, gathering the materials for submission, and learn how to represent their data in the BCO, as well as meetings and documentation for the pilot project.

Groups are asked to meet with us to explain difficulties working with the standard. Groups may decide to meet with us individually, if they desire, rather than as part of a larger meeting with the other groups.

=== Challenges and Solutions ===
During development and maintenance of the platform, users may run into bugs and may have suggestions regarding the user interface (UI). To address these challenges, users can submit their feedback and report issues via the website's [https://github.com/biocompute-objects/portal_userdb/issues/new/choose 'Report an Issue'] link. This feedback is useful in refining the platform and enhancing the overall user experience. Additionally, to ensure continuous effectiveness and functionality of BioCompute Objects (BCOs), regular updates and enhancements are made based on testing and user feedback.

== References and Resources ==
For additional information, please refer to the resources below:

* [https://wiki.biocomputeobject.org/index.php?title=Main_Page BioCompute Objects Wiki]
* [https://wiki.biocomputeobject.org/White_paper White Paper]

=== Contact ===
For any questions or to participate in the pilot, please email Jonathon Keeney, project co-PI at George Washington University: keeneyjg@gwu.edu

BCO Pilot Project

2024-05-20T16:50:16Z

ChinweokeO: /* Challenges and Solutions */

== Pilot Project ==
BioCompute is shorthand for IEEE 2791-2020, a [https://standards.ieee.org/ieee/2791/7337/ standard for communicating computational workflows]. The standard was developed in response to difficulties in recording and interpreting bioinformatics pipelines. BioCompute is a framework for step by step description of computational workflows. BioCompute defines what content must be included, and what form it should take. It includes data provenance and rich metadata to eliminate ambiguity. The standard also includes an “Execution Domain” for re-executing a pipeline, if desired.

Three Centers at the FDA [https://www.federalregister.gov/documents/2020/07/22/2020-15771/electronic-submissions-data-standards-support-for-the-international-institute-of-electrical-and have adopted the standard] (see notice in Federal Registry by the Food and Drug Administration on 07/22/2020) for bioinformatics applications. To increase adoption of BioCompute and bring awareness within and outside of FDA we propose a pilot with the BioCompute team, FDA and industry. Because the standard was developed to manage complexity and reduce the organizational burden on FDA reviewers and regulated industry submitting to them, the purpose of this pilot project is to bring both sides in agreement around its usage thereby streamlining and standardizing computational workflow submissions and reviews. Participating sponsors will prepare and submit a computational workflow with a BioCompute Object (BCO) without any additional clarification, and FDA reviewers will review the BCO. Initial planning meetings, gathering project materials, preparing and submitting BCOs, BCO review, and final debrief are expected to take one year.

== Expected Outcome ==

=== Documentation and Reporting ===
Throughout the process, we will document anything that is difficult to understand, barriers to working with or reading the BCO, and any other general issues. As a result, a [https://wiki.biocomputeobject.org/Best_Practices best practices document] and [https://wiki.biocomputeobject.org/Security_Plan security plan] have been generated to support the standard and there may be additional training materials, created as needed to enable a group to prepare or read a BCO with minimal training. These resources are meant to support the standard as a vehicle for more fluid communication, and to enable a group to prepare or read a BCO with minimal training.

In addition, groups that participate in the pilot will have first-hand knowledge of submitting computational analyses and how to do so efficiently. Monthly reports are also submitted to maintain communication of plans and processes as they occur.

== Request ==

=== Collaboration and Communication ===
To have the most impact, this project requires input from multiple groups with close collaboration with FDA-HIVE team. We’re asking FDA reviewers who review any work that contains a computational pipeline to participate. Examples of computational pipelines include a medical device for the detection of physiological warning signs, a diagnostic test for the presence of pathogenic species, supporting evidence for a new drug application in the form of NGS analyses, or others.

Only the computational portion need be submitted, and participants will use their own data for submission. Data submitted need not be actual clinical data, however, the more similar the data to a real submission, the more valuable the pilot. Participating FDA reviewers will be asked to review the pilot submission with no additional input, and to document anything they feel is unclear or not presented well.

Participating sponsors are asked to prepare realistic regulatory submissions using one or more BCOs to describe their work. We estimate that the project will require some level of effort from all participants. The representative(s) will be involved in planning, gathering the materials for submission, and learn how to represent their data in the BCO, as well as meetings and documentation for the pilot project.

Groups are asked to meet with us to explain difficulties working with the standard. Groups may decide to meet with us individually, if they desire, rather than as part of a larger meeting with the other groups.

=== Challenges and Solutions ===
During development and maintenance of the platform, users may run into bugs and may have suggestions regarding the user interface (UI). To address these challenges, users can submit their feedback and report issues via the website's [https://github.com/biocompute-objects/portal_userdb/issues/new/choose 'Report an Issue'] link. This feedback is useful in refining the platform and enhancing the overall user experience. Additionally, to ensure continuous effectiveness and functionality of BioCompute Objects (BCOs), regular updates and enhancements based on testing and user feedback.

== References and Resources ==
For additional information, please refer to the resources below:

* [https://wiki.biocomputeobject.org/index.php?title=Main_Page BioCompute Objects Wiki]
* [https://wiki.biocomputeobject.org/White_paper White Paper]

=== Contact ===
For any questions or to participate in the pilot, please email Jonathon Keeney, project co-PI at George Washington University: keeneyjg@gwu.edu

BCO Pilot Project

2024-05-20T16:49:43Z

ChinweokeO:

== Pilot Project ==
BioCompute is shorthand for IEEE 2791-2020, a [https://standards.ieee.org/ieee/2791/7337/ standard for communicating computational workflows]. The standard was developed in response to difficulties in recording and interpreting bioinformatics pipelines. BioCompute is a framework for step by step description of computational workflows. BioCompute defines what content must be included, and what form it should take. It includes data provenance and rich metadata to eliminate ambiguity. The standard also includes an “Execution Domain” for re-executing a pipeline, if desired.

Three Centers at the FDA [https://www.federalregister.gov/documents/2020/07/22/2020-15771/electronic-submissions-data-standards-support-for-the-international-institute-of-electrical-and have adopted the standard] (see notice in Federal Registry by the Food and Drug Administration on 07/22/2020) for bioinformatics applications. To increase adoption of BioCompute and bring awareness within and outside of FDA we propose a pilot with the BioCompute team, FDA and industry. Because the standard was developed to manage complexity and reduce the organizational burden on FDA reviewers and regulated industry submitting to them, the purpose of this pilot project is to bring both sides in agreement around its usage thereby streamlining and standardizing computational workflow submissions and reviews. Participating sponsors will prepare and submit a computational workflow with a BioCompute Object (BCO) without any additional clarification, and FDA reviewers will review the BCO. Initial planning meetings, gathering project materials, preparing and submitting BCOs, BCO review, and final debrief are expected to take one year.

== Expected Outcome ==

=== Documentation and Reporting ===
Throughout the process, we will document anything that is difficult to understand, barriers to working with or reading the BCO, and any other general issues. As a result, a [https://wiki.biocomputeobject.org/Best_Practices best practices document] and [https://wiki.biocomputeobject.org/Security_Plan security plan] have been generated to support the standard and there may be additional training materials, created as needed to enable a group to prepare or read a BCO with minimal training. These resources are meant to support the standard as a vehicle for more fluid communication, and to enable a group to prepare or read a BCO with minimal training.

In addition, groups that participate in the pilot will have first-hand knowledge of submitting computational analyses and how to do so efficiently. Monthly reports are also submitted to maintain communication of plans and processes as they occur.

== Request ==

=== Collaboration and Communication ===
To have the most impact, this project requires input from multiple groups with close collaboration with FDA-HIVE team. We’re asking FDA reviewers who review any work that contains a computational pipeline to participate. Examples of computational pipelines include a medical device for the detection of physiological warning signs, a diagnostic test for the presence of pathogenic species, supporting evidence for a new drug application in the form of NGS analyses, or others.

Only the computational portion need be submitted, and participants will use their own data for submission. Data submitted need not be actual clinical data, however, the more similar the data to a real submission, the more valuable the pilot. Participating FDA reviewers will be asked to review the pilot submission with no additional input, and to document anything they feel is unclear or not presented well.

Participating sponsors are asked to prepare realistic regulatory submissions using one or more BCOs to describe their work. We estimate that the project will require some level of effort from all participants. The representative(s) will be involved in planning, gathering the materials for submission, and learn how to represent their data in the BCO, as well as meetings and documentation for the pilot project.

Groups are asked to meet with us to explain difficulties working with the standard. Groups may decide to meet with us individually, if they desire, rather than as part of a larger meeting with the other groups.

=== Challenges and Solutions ===
During development and maintenance of the platform, users may run into bugs and may have suggestions regarding the user interface (UI). To address these challenges, users can submit their feedback and report issues via the website's [https://github.com/biocompute-objects/portal_userdb/issues/new/choose 'Report an Issue'] link. This feedback is useful in refining the platform and enhancing the overall user experience. Additionally, to ensure continuous effectiveness and functionality of BioCompute Objects (BCOs), regular updates and enhancements based on testing user feedback.

== References and Resources ==
For additional information, please refer to the resources below:

* [https://wiki.biocomputeobject.org/index.php?title=Main_Page BioCompute Objects Wiki]
* [https://wiki.biocomputeobject.org/White_paper White Paper]

=== Contact ===
For any questions or to participate in the pilot, please email Jonathon Keeney, project co-PI at George Washington University: keeneyjg@gwu.edu

BCO Pilot Project

2024-05-20T16:09:29Z

ChinweokeO: /* Expected Outcome */

BCO Pilot Project

2024-05-20T15:44:44Z

ChinweokeO: /* Pilot Project */

Best Practices

2024-05-20T15:42:11Z

ChinweokeO: /* BCO Creation and Versioning */

The primary goal of this guide is to offer comprehensive guidance for effectively using and maintaining BioCompute Objects in the fields of bioinformatics and computational biology. This includes promoting consistency, data integrity, and collaboration among professionals, while supporting regulatory compliance and enhancing usability and adoption. Furthermore, it aims to facilitate the ongoing maintenance and updates of BCOs to ensure their continued relevance and usability across different computational domains

== General ==

*The required domains are defined by the IEEE. However, a BioCompute Object is considered complete when an Error Domain exists.
*Versioning is allowed, but only if the changes do not affect the workflow or output. BCO versioning follows a minor.patch schema, no major versions are allowed (substantial changes result in a new BCO). Minor changes are things like a change of contact information for a contributor, patch changes are things like spelling and grammar fixes.
*In general, any step that does not transform data does not need to be included in the Description Domain as a formal step, and can be described instead in the Usability Domain. For example, arranging rows and columns in a table, or formatting a figure. Steps that transform data should comprise their own step in the Description Domain.
*The Usability Domain should contain enough information to enable a naïve user generally skilled in bioinformatics to understand the analysis. This means that references to commonly used resources (such as basic Unix commands, well-known databases like NCBI, basic terms like “alignment,” etc.) do not need to be explained, but references to less well-known resources (such as obscure python packages, etc.) should be described. The description should be tailored to the intended audience, and BCOs intended for public consumption should assume a basic level of bioinformatics proficiency.

== BioCompute Registry ==

The [https://biocomputeobject.org/login BioCompute Registry] is a domain registry for BCO IDs in which users can register their institution or organization. Similar to a website registry, this will allow the owner of that domain to use any domain organization of their choosing, and prevent naming collisions between groups. For example, the owner of “GW” can build BCOs GW_0001.1, GW01A, GW_, or any other naming system of their preference, and these will not conflict with another registered domain, such as FDA_0001.1, etc. The BCO Registry registration numbers may not exceed five characters and are recommended to be three characters. Any alphanumeric characters are acceptable.

A [[Main Page|BCO]] may be registered only by the author of the object, and the domain must be approved by the domain holder. Until automated systems are in place, register a BCO by sending the BCO ID and email of the registrant to the [BioCompute Team](mailto:keeneyjg@gwu.edu). The following institutional domains have been reserved:
*GWU
*FDA
*NIH
*CDC
*NCI

== BCO Creation and Versioning ==
''Intended Audience: BCO authors''

* BioCompute IDs are used as persistent URLs. A novel usability domain must result in the creation of a new BCO with a new BCO ID. BCO IDs are immutable upon creation, and are never deleted or retired. If the usability domain (UD) remains unchanged, this results in a new version of the BCO. BCO ID example: OMX_000001
* BCO major and minor versions can be incremented based on project/institution documented policies.
* The BioCompute consortium maintains a database of registered authorities. Registered authorities are able to assign their reserved prefixes to their own IDs in the object_id field, such as OMX_000001. We encourage that everyone registers a prefix at biocomputeobject.org.

== Preferred Ontologies ==
=== Semantic Versioning ===
BCO versioning should adhere to [https://semver.org/ semantic versioning] to establish how version numbers are assigned and incremented. Given a version number MAJOR.MINOR.PATCH, when versioning a BCO increment the:

1.MAJOR version when you make incompatible API changes

2.MINOR version when you add functionality in a backward-compatible manner

3.PATCH version when you make backward-compatible bug fixes. Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.

=== PAV Ontology and PROV-O ===

To preserve the provenance of each BCO, the contribution type of the reviewers and contributors is a choice taken from PAV ontology: provenance, authoring, and versioning, which also maps to the PROV-O. The following are possible values for the status of an object in the review process:

*unreviewed flag indicates that the object has been submitted, but no further evaluation or verification has occurred.
*in-review flag indicates that verification is underway.
*approved flag indicates that the BCO has been verified and reviewed.
*suspended flag indicates an object that was once valid is no longer considered valid.
*rejected flag indicates that an error or inconsistency was detected in the BCO, and it has been removed or rejected.

=== Namespace: CURIE ===

The external references field contains a list of the databases and/or ontology IDs that are cross-referenced in the BCO. The external references are used to provide more specificity in the information related to BCO entries. Cross-referenced resources need to be available in the public domain. The external references are stored in the form of prefixed identifiers (CURIEs). These CURIEs map directly to the URIs maintained by identifiers.org. See Section 3.5 for a list of the CURIEs used in this example.

== BCO Metadata ==
The three metadata fields are filled out at the time of submission. Validity check fills in the <code>spec_version</code> with the IEEE URL, an option to run a SHA256 (or just input your own hash value) for <code>etag</code>, and <code>object_id</code> is assigned (with option to choose from any prefix associated with the account).

== Domain-specific guidance ==
'''The following fields are optional based on the IEEE-2791-2020 standard:''' ''Extension Domain, Parametric Domain, Error Domain.''

=== ''[https://wiki.biocomputeobject.org/index.php?title=Provenance-domain Provenance Domain]'' ===
This domain serves as a repository for metadata describing the BCO.

=== ''[https://wiki.biocomputeobject.org/index.php?title=Usability-domain Usability Domain]'' ===
Authors have access to a text field where they can provide a comprehensive description of the analysis and relevant details.

=== ''[https://wiki.biocomputeobject.org/index.php?title=Extension-domain Extension Domain]'' ===
Format of how the schema would be defined: Execution domain

=== ''[https://wiki.biocomputeobject.org/index.php?title=Description-domain Description Domain]'' ===
It includes a detailed breakdown of the individual steps involved, the external resources essential for each step, and the relationships between input and output objects.

=== ''[https://wiki.biocomputeobject.org/index.php?title=Execution-domain Execution Domain]'' ===
When recording manual curation, the <code>script</code> field of the <code>execution_domain</code> should link to a Google Document or GitHub markdown that describes the steps, either programmatically or in a stepwise fashion. Manual curation steps should ALSO be properly documented in the <code>description_domain</code>. An easy way to conceptualize this is: Description domain is for people, Execution domain is for machine (or programmers).

=== ''[https://wiki.biocomputeobject.org/index.php?title=Parametric-domain Parametric Domain]'' ===
This domain captures any modifications made to parameters from their default values.

=== ''[https://wiki.biocomputeobject.org/index.php?title=Iodomain Input and Output Domain]'' ===
This domain serves as a catalog of global input and output files used in the analysis.

=== ''[https://wiki.biocomputeobject.org/index.php?title=Error-domain Error domain]'' ===
This domain can support a “QA/QC rules” subdomain which provides rules that, if the output file does not pass the appropriate criteria, then it is flagged as an error.
== BCO Form-based portal ==
''Intended Audience: BCO tool developers and authors''

BCOs can be created using any bioinformatics platform that has BCO read and write functionalities. For users who do not have access to a bioinformatics platform they can use the BCO Builder in the BCO Portal which has some of the basic API functionalities:

* Create a BCO that is conformant to IEEE-2791.
* Download and install an instance within an organization’s firewall
* View videos and documentation on tool use

__FORCETOC__

Best Practices

2024-05-20T15:39:07Z

ChinweokeO:

The primary goal of this guide is to offer comprehensive guidance for effectively using and maintaining BioCompute Objects in the fields of bioinformatics and computational biology. This includes promoting consistency, data integrity, and collaboration among professionals, while supporting regulatory compliance and enhancing usability and adoption. Furthermore, it aims to facilitate the ongoing maintenance and updates of BCOs to ensure their continued relevance and usability across different computational domains

== General ==

*The required domains are defined by the IEEE. However, a BioCompute Object is considered complete when an Error Domain exists.
*Versioning is allowed, but only if the changes do not affect the workflow or output. BCO versioning follows a minor.patch schema, no major versions are allowed (substantial changes result in a new BCO). Minor changes are things like a change of contact information for a contributor, patch changes are things like spelling and grammar fixes.
*In general, any step that does not transform data does not need to be included in the Description Domain as a formal step, and can be described instead in the Usability Domain. For example, arranging rows and columns in a table, or formatting a figure. Steps that transform data should comprise their own step in the Description Domain.
*The Usability Domain should contain enough information to enable a naïve user generally skilled in bioinformatics to understand the analysis. This means that references to commonly used resources (such as basic Unix commands, well-known databases like NCBI, basic terms like “alignment,” etc.) do not need to be explained, but references to less well-known resources (such as obscure python packages, etc.) should be described. The description should be tailored to the intended audience, and BCOs intended for public consumption should assume a basic level of bioinformatics proficiency.

== BioCompute Registry ==

The [https://biocomputeobject.org/login BioCompute Registry] is a domain registry for BCO IDs in which users can register their institution or organization. Similar to a website registry, this will allow the owner of that domain to use any domain organization of their choosing, and prevent naming collisions between groups. For example, the owner of “GW” can build BCOs GW_0001.1, GW01A, GW_, or any other naming system of their preference, and these will not conflict with another registered domain, such as FDA_0001.1, etc. The BCO Registry registration numbers may not exceed five characters and are recommended to be three characters. Any alphanumeric characters are acceptable.

A [[Main Page|BCO]] may be registered only by the author of the object, and the domain must be approved by the domain holder. Until automated systems are in place, register a BCO by sending the BCO ID and email of the registrant to the [BioCompute Team](mailto:keeneyjg@gwu.edu). The following institutional domains have been reserved:
*GWU
*FDA
*NIH
*CDC
*NCI

== Preferred Ontologies ==
=== Semantic Versioning ===
BCO versioning should adhere to [https://semver.org/ semantic versioning] to establish how version numbers are assigned and incremented. Given a version number MAJOR.MINOR.PATCH, when versioning a BCO increment the:

1.MAJOR version when you make incompatible API changes

2.MINOR version when you add functionality in a backward-compatible manner

3.PATCH version when you make backward-compatible bug fixes. Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.

=== PAV Ontology and PROV-O ===

To preserve the provenance of each BCO, the contribution type of the reviewers and contributors is a choice taken from PAV ontology: provenance, authoring, and versioning, which also maps to the PROV-O. The following are possible values for the status of an object in the review process:

*unreviewed flag indicates that the object has been submitted, but no further evaluation or verification has occurred.
*in-review flag indicates that verification is underway.
*approved flag indicates that the BCO has been verified and reviewed.
*suspended flag indicates an object that was once valid is no longer considered valid.
*rejected flag indicates that an error or inconsistency was detected in the BCO, and it has been removed or rejected.

=== Namespace: CURIE ===

The external references field contains a list of the databases and/or ontology IDs that are cross-referenced in the BCO. The external references are used to provide more specificity in the information related to BCO entries. Cross-referenced resources need to be available in the public domain. The external references are stored in the form of prefixed identifiers (CURIEs). These CURIEs map directly to the URIs maintained by identifiers.org. See Section 3.5 for a list of the CURIEs used in this example.

== BCO Creation and Versioning ==
''Intended Audience: BCO authors''

* BioCompute IDs are used as persistent URLs. A novel usability domain must result in the creation of a new BCO with a new BCO ID. BCO IDs are immutable upon creation, and are never deleted or retired. If the usability domain (UD) remains unchanged, this results in a new version of the BCO. BCO ID example: OMX_000001
* BCO major and minor versions can be incremented based on project/institution documented policies.
* The BioCompute consortium maintains a database of registered authorities. Registered authorities are able to assign their reserved prefixes to their own IDs in the object_id field, such as OMX_000001. We encourage that everyone registers a prefix at biocomputeobject.org.

== BCO Metadata ==
The three metadata fields are filled out at the time of submission. Validity check fills in the <code>spec_version</code> with the IEEE URL, an option to run a SHA256 (or just input your own hash value) for <code>etag</code>, and <code>object_id</code> is assigned (with option to choose from any prefix associated with the account).

== Domain-specific guidance ==
'''The following fields are optional based on the IEEE-2791-2020 standard:''' ''Extension Domain, Parametric Domain, Error Domain.''

=== ''[https://wiki.biocomputeobject.org/index.php?title=Provenance-domain Provenance Domain]'' ===
This domain serves as a repository for metadata describing the BCO.

=== ''[https://wiki.biocomputeobject.org/index.php?title=Usability-domain Usability Domain]'' ===
Authors have access to a text field where they can provide a comprehensive description of the analysis and relevant details.

=== ''[https://wiki.biocomputeobject.org/index.php?title=Extension-domain Extension Domain]'' ===
Format of how the schema would be defined: Execution domain

=== ''[https://wiki.biocomputeobject.org/index.php?title=Description-domain Description Domain]'' ===
It includes a detailed breakdown of the individual steps involved, the external resources essential for each step, and the relationships between input and output objects.

=== ''[https://wiki.biocomputeobject.org/index.php?title=Execution-domain Execution Domain]'' ===
When recording manual curation, the <code>script</code> field of the <code>execution_domain</code> should link to a Google Document or GitHub markdown that describes the steps, either programmatically or in a stepwise fashion. Manual curation steps should ALSO be properly documented in the <code>description_domain</code>. An easy way to conceptualize this is: Description domain is for people, Execution domain is for machine (or programmers).

=== ''[https://wiki.biocomputeobject.org/index.php?title=Parametric-domain Parametric Domain]'' ===
This domain captures any modifications made to parameters from their default values.

=== ''[https://wiki.biocomputeobject.org/index.php?title=Iodomain Input and Output Domain]'' ===
This domain serves as a catalog of global input and output files used in the analysis.

=== ''[https://wiki.biocomputeobject.org/index.php?title=Error-domain Error domain]'' ===
This domain can support a “QA/QC rules” subdomain which provides rules that, if the output file does not pass the appropriate criteria, then it is flagged as an error.
== BCO Form-based portal ==
''Intended Audience: BCO tool developers and authors''

BCOs can be created using any bioinformatics platform that has BCO read and write functionalities. For users who do not have access to a bioinformatics platform they can use the BCO Builder in the BCO Portal which has some of the basic API functionalities:

* Create a BCO that is conformant to IEEE-2791.
* Download and install an instance within an organization’s firewall
* View videos and documentation on tool use

__FORCETOC__

BCO Pilot Project

2024-05-20T14:28:53Z

ChinweokeO:

== BioCompute Objects (BCOs) ==
A BioCompute Object (BCO) is an instance of the BioCompute standard and is a computational record of a bioinformatics pipeline. A BCO is not an analysis but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result and includes additional metadata to identify provenance and usage.

== Pilot Project ==
The BioCompute pilot project aims to increase adoption and awareness of the purpose of BioCompute Objects (BCOs) both within and outside of the FDA. This involves the collaboration among the BioCompute team, FDA and industry. It is significant in fostering mutual agreement on the usage of BCOs thereby streamlining and standardizing computational workflow submissions and reviews.

Participating sponsors will prepare and submit a computational workflow with a BioCompute Object (BCO) without any additional clarification, and FDA reviewers will review the BCO.

=== Documentation and Reporting ===
Documentation Guidelines

Regulatory Compliance

Standards and Best Practices

=== Collaboration and Communication ===
Stakeholders

Communication Plan & Collaboration Tools

=== Challenges and Solutions ===
Common Challenges

Solutions and Mitigations

Future Directions

== References and Resources ==
[https://wiki.biocomputeobject.org/White_paper White Paper]

BioCompute Conference and Workshop

2024-05-20T13:47:04Z

ChinweokeO: /* Conference Webinar */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Keeney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>
== <big>Conference Webinar</big> ==
<big>''BioCompute Conference 2024 at FDA''</big>

<big>''Presented by the BioCompute team with plenary address by CBER Director Dr. Peter Marks''</big>

<big>'''Published May 10, 2024'''</big>

[https://www.youtube.com/watch?v=gD3c9ZVT-Uw '''Watch Here''']

00:00 Intro - Dr. Keeney

11:45 Vision and Future of Biocompute - Dr. Mazumder

28:48 FDA Alignment With The Vision of Biocompute - Peter Marks

43:23 Biocompute Vision From an FDA-Industry Perspective - Dr. Vahan Simonyan

1:00:26 A computational framework for end-to-end clinical omics analysis - Jun Luo

1:10:47 Applications of Biocompute Objects For Viral Metagenomics Analysis - Julia Maritz

1:21:23 Question Panel 1 1:42:14 Biocompute Objects and Workflows - Mark Walderhaug

1:59:40 Computational Reviews at CBER - Luis V Santanz-Quintero

2:12:23 High Throughput Sequencing Data Challenges in FDA Regulatory Review - Eric Donaldson

2:30:26 Question Panel 2:

2:43:43 AI and Data Science For Health and Research: Exploring NIH Strategies, Challenges, and Visions for the Future - Susan Gregurick

3:02:32 Biocompute Object Submissions to FDA - Ginny Hussong

3:15:17 Extending BCO Specification into a Generic Metamodel For Computable Data - Guangzhi Sun

3:37:17 Functioning Biocompute Objects As AI Agents - Jonas S Almeida

3:52:20 DNAnexus: Democratizing access to BCOs with the BCOnexus Platform Free Editor - Sam Westreich

4:06:09 Facilitating BCO Use From Standard to Best Practices: The Neoantigen Use Case - Dennis A. Dean

4:28:52 BioCompute Portal, BioCompute Database, and User Database: Why So Many? - Charles Hadley King

4:50:00 BCO Provenance Models and FAIR Computational Workflows - Stain Soiland-Reyes & Meznah Aloqalaa

5:10:51 Generating BCO’s For Nextflow Pipelines - Ben Sherman

05:36:32 Large Language Models - Konstantinos Krampis

05:51:10 Retrieval-Augmented Generation For BioCompute Object Creation - Sean Kim

06:07:28 BioCompute Library Project - Sean Keeney

06:11:54 Visualization For Published BCOs - Tianyi Wang

06:16:16 BCOs to Unite Data and Workflow into Analysis - Dr. Patrick McNeely

06:19:20 Closing Remarks - Dr. Mazumder & Mark Walderhaug

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:10 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Hadley King'''
<small>Research Scientist, HIVE Lab, George Washington University</small>
|BioCompute Portal, BioCompute Database, and User Database: Why so many?
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Virginia Hussong.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Virginia Hussong</div></big>
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:HadleyKing.png|alt=Headshot for Hadley King|center|thumb|200x200px]]<big><div style="text-align: center;">Hadley King</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|[[File:Julia Maritz.jpg|none|thumb|204x204px]]<big><div style="text-align: center;">Julia Maritz</div></big>
|}

== <big>Use Case Collection Form</big>==
<big>Please take a moment to fill out our use case collection form here: https://docs.google.com/forms/d/e/1FAIpQLSfS5E-cpPMvIdEHVqPiZnmcpsH5JetMsBAY2vnsemRWeDj5uw/viewform </big>

==<big>Contact Us</big>==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BCO Pilot Project

2024-05-20T11:43:49Z

ChinweokeO: /* Documentation and Reporting */

== Introduction ==
The BioCompute pilot project aims to increase adoption and awareness of the purpose of BioCompute Objects (BCOs) both within and outside of the FDA. This involves the collaboration among the BioCompute team, FDA and industry. It is significant in fostering mutual agreement on the usage of BCOs thereby streamlining and standardizing computational workflow submissions and reviews.

Participating sponsors will prepare and submit a computational workflow with a BioCompute Object (BCO) without any additional clarification, and FDA reviewers will review the BCO.

== BioCompute Objects (BCOs) ==
A BioCompute Object (BCO) is an instance of the BioCompute standard and is a computational record of a bioinformatics pipeline. A BCO is not an analysis but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result and includes additional metadata to identify provenance and usage.

== Pilot Project ==
Description

=== Documentation and Reporting ===
Documentation Guidelines

Regulatory Compliance

Standards and Best Practices

=== Collaboration and Communication ===
Stakeholders

Communication Plan & Collaboration Tools

=== Challenges and Solutions ===
Common Challenges

Solutions and Mitigations

Future Directions

== References and Resources ==
[https://wiki.biocomputeobject.org/White_paper White Paper]

BCO Pilot Project

2024-05-20T11:42:56Z

ChinweokeO: /* BioCompute Objects (BCOs) */

== Introduction ==
The BioCompute pilot project aims to increase adoption and awareness of the purpose of BioCompute Objects (BCOs) both within and outside of the FDA. This involves the collaboration among the BioCompute team, FDA and industry. It is significant in fostering mutual agreement on the usage of BCOs thereby streamlining and standardizing computational workflow submissions and reviews.

Participating sponsors will prepare and submit a computational workflow with a BioCompute Object (BCO) without any additional clarification, and FDA reviewers will review the BCO.

== BioCompute Objects (BCOs) ==
A BioCompute Object (BCO) is an instance of the BioCompute standard and is a computational record of a bioinformatics pipeline. A BCO is not an analysis but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result and includes additional metadata to identify provenance and usage.

== Pilot Project ==
Description

=== Documentation and Reporting ===
Standard Operating Procedures (SOPs)

Documentation Guidelines

Reporting Results

Compliance and Standards

Regulatory Compliance

Standards and Best Practices

=== Collaboration and Communication ===
Stakeholders

Communication Plan

Collaboration Tools

=== Challenges and Solutions ===
Common Challenges

Solutions and Mitigations

Future Directions

Next Steps

== References and Resources ==
[https://wiki.biocomputeobject.org/White_paper White Paper]

BCO Pilot Project

2024-05-20T03:13:36Z

ChinweokeO: /* Introduction */

BCO Pilot Project

2024-05-20T03:02:59Z

ChinweokeO: Created page with "== Introduction == Overview: Briefly introduce the BioCompute Pilot Project, its purpose, and significance. Objectives: Outline the key goals and objectives of the project. Scope: Define the scope of the project, including the types of data and analyses involved. == BioCompute Objects (BCOs) == What is a BCO?: Provide a detailed explanation of BioCompute Objects, including their purpose and components. Structure of a BCO: Break down the sections of a BCO, such as Pro..."

== Introduction ==
Overview: Briefly introduce the BioCompute Pilot Project, its purpose, and significance.

Objectives: Outline the key goals and objectives of the project.

Scope: Define the scope of the project, including the types of data and analyses involved.

== BioCompute Objects (BCOs) ==
What is a BCO?: Provide a detailed explanation of BioCompute Objects, including their purpose and components.

Structure of a BCO: Break down the sections of a BCO, such as Provenance Domain, Usability Domain, Extension Domain, Description Domain, and Execution Domain.

Examples: Provide examples of BCOs relevant to the pilot project.

== Pilot Project ==
Pipeline Description: Describe the bioinformatics pipelines being tested or implemented in the pilot project.

Step-by-Step Process: Outline the steps involved in the pipeline, including data preprocessing, analysis, and post-processing.

Tools and Software: List the bioinformatics tools and software used in each step of the pipeline.

Data Management

Data Sources: Detail the sources of the data used in the pilot project (e.g., TCGA, GTEx, 1000 Genomes).

Data Formats: Describe the formats of the data (e.g., FASTQ, BAM, VCF) and how they are handled.

Data Storage: Explain how data is stored, managed, and accessed.

=== Documentation and Reporting ===
Standard Operating Procedures (SOPs): Include any SOPs related to the project.

Documentation Guidelines: Provide guidelines for documenting the bioinformatics workflows and results.

Reporting Results: Outline how results are reported, including any templates or standards used.

Compliance and Standards

Regulatory Compliance: Discuss any regulatory requirements relevant to the project (e.g., FDA guidelines).

Standards and Best Practices: Highlight the standards and best practices followed in the project (e.g., FAIR data principles).

=== Collaboration and Communication ===
Stakeholders: Identify the key stakeholders involved in the project.

Communication Plan: Outline the plan for communication among team members and with external stakeholders.

Collaboration Tools: List the tools and platforms used for collaboration (e.g., GitHub, Slack, Google Drive).

=== Challenges and Solutions ===
Common Challenges: Discuss common challenges encountered during the project.

Solutions and Mitigations: Describe the solutions implemented to address these challenges.

Future Directions

Next Steps: Outline the next steps and future plans for the pilot project.

Potential Expansions: Discuss potential expansions of the project or new areas of research.

== References and Resources ==
Literature: Provide references to relevant literature and publications.

Resources: List any additional resources, such as tutorials, guides, or external links that are useful for understanding and participating in the project.

Main Page

2024-05-16T00:59:16Z

ChinweokeO:

{{DISPLAYTITLE:<span style="position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);">{{FULLPAGENAME}}</span>}}
__NOTOC__

<div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;">
<div style="margin:0.4em; text-align:center;">
<div style="font-size:160%; padding:.1em;">Welcome to BioCompute Objects Wiki,</div>
<div style="font-size:100%;">The [https://www.mediawiki.org/wiki/MediaWiki MediaWiki] for the BioCompute Objects project. This wiki system provides complementary information to the [https://www.biocomputeobject.org/ BioCompute portal] and is divided into the following main sections: General information for the [https://www.biocomputeobject.org/ BioCompute portal], [[User_guide|Quick Start and User Guide]], [[Faq|FAQ]], [[Sop|Curation SOP]], and [[About|About]] for the [https://www.biocomputeobject.org/ BioCompute portal].</div>You can also find the BioCompute White paper [[White paper|here]].
</div>
</div>
<div style="clear: both;"></div>

<div style="clear: both;"><br />
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
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<h3>[[User guide|BioCompute Object (BCO) User Guide]]</h3>
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
This document specifies the structure of BioCompute Objects. The specification is split into multiple parts linked to this top-level document and is maintained in a [https://github.com/biocompute-objects/BCO_Specification GitHub repository] where contributions are welcome. This document was created by the [[Main_Page#BioCompute_Object_Consortium_members_(BCOC)|BioCompute Object Consortium members (BCOC)]].

It is offered as support for IEEE-2791-2020: [https://standards.ieee.org/ieee/2791/7337/ IEEE Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication].

Read more: [[Introduction|Introduction to BioCompute Objects]]

</div>
</div>

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<h3>[https://wiki.biocomputeobject.org/index.php?title=FAQs Frequently Asked Questions]</h3>
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
The FAQ section contains a list of questions asked by users regarding using the portal, pipeline steps, and extensions as well as questions related to the prerequisite, knowledgebase recommendation, and saving and publishing BCOs.

Read more: [[Bco faq|Frequently Asked Questions]]

</div>
</div>

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<h3>[[Sop|BCO Curation SOP]]</h3>
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
Intended audience: authors and developers

This section is intended to provide guidance on BCO™ creation, versioning, certification and authentication.

Read more: [[Sop|BCO Curation SOP]]

</div>
</div>
</div>
</div>

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<h3>[[BioCompute Conference and Workshop|Workshop]]</h3>
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
We are hosting an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].
</div>
</div>

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<h3>[[About]]</h3>
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
A BioCompute Object (BCO) is an instance of the BioCompute standard and is a computational record of a bioinformatics pipeline. A BCO is not an analysis but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result and includes additional metadata to identify provenance and usage.

Read more:
*[[About|What is BioCompute?]]
*[[About|Wifi Analogy]]
*[[About|BioCompute Description]]
</div>
</div>

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<h3>[[Publications|Publication]]</h3>
<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
'''For Citation Purpose:''' Simonyan, V., Goecks, J., & Mazumder, R. (2017). Biocompute Objects — A Step towards Evaluation and Validation of Biomedical Scientific Computations. PDA Journal of Pharmaceutical Science and Technology, 71(2), 136–146. doi: 10.5731/pdajpst.2016.006734

See also full list of [[publications]] about BioCompute Object.

=== Other links ===
# [[CDISC]]
# [[Galaxy]]
# [[RO-Crate]]
# [[CWL|Common Workflow Language (CWL)]]
# [https://fairsharing.org/4293 FAIRsharing]
</div>
</div>

FAQs

2024-05-15T20:07:25Z

ChinweokeO:

'''Go back to [[Main Page|BioCompute Objects]].'''

== General ==
1. '''How can I build a BioCompute Object (BCO)?'''

You have several options for building a BCO. You can use the standalone "builder" tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.

2. '''What are the minimum requirements for conformance with the BioCompute standard?'''

The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.

3. '''How can I ensure my submission validates against the BioCompute schema?'''

Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].

4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].

5. '''Can you provide an example of a completed BioCompute Object (BCO)?'''

Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.

6. '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''

Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.

7. '''How can a third-party access URIs in a BCO?'''

URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all.

8. '''What is a SHA1 Checksum?'''

A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.

9. '''How do I sign in with an ORCID/What is an ORCID?'''

[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID, create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.

== Pipeline Questions ==

1. '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''

The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).

2. '''What is the nf-core plugin and how can I test it?'''

The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:

* Ensure you have the latest version of the plugin installed.

* Add the following code snippets to your Nextflow configuration file:

plugins {

id 'nf-prov'

}

prov.enabled = true

prov {

formats {

bco {

file = 'bco.json'

overwrite = true

}

}

}

These settings will enable the BCO format and specify the output file as "bco.json". Ensure you include these snippets in your configuration file to activate the BCO format.

For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]

== Inputs and Outputs ==

1. '''What is the relationship and difference between input_list in description_domain and input_subdomain? Does input_subdomain contain all the input files of all the pipeline steps?'''

Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.

2. '''What is the relationship and difference between output_list in description_domain and output_subdomain? Does output_subdomain contain all the output files of all the pipeline steps?'''

The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.

3. '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''

Yes they are, the timestamp is used for creation in those cases.

4. '''Can a script from the execution domain also be considered an input?'''

This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.

== Extensions ==

1. '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''

Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.

2. '''How can BCOs be used for knowledgebases?'''

Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.

BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.

The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.

== Prerequisites ==

1. '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''

Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.

== Knowledgebases ==

1. '''Can BCOs be used for curating databases?'''

Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.

Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.

BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.

The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.

== Saving and Publishing a BCO ==

1. '''Why is my BCO not saved after clicking '''SAVE'''?'''

The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.

2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''

A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.

== BCO Validation and Error messages ==

The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.

1. '''"[description_domain][pipeline_steps][0][step_number]": "'1' is not of type 'integer'"'''

The '''step_number''' in the BCO JSON needs to be an INTEGER.

This means it can not be in quotes like this:
''' "step_number": "1",'''
Instead, it must be represented like this:
''' "step_number": 1,'''

You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.

== Submitting BCOs to FDA ==

# '''How should I submit a BCO with a regulatory submission?''' A BCO file can be saved as a plain text (".txt") document and submitted with a regulatory submission. You can inform the reviewer that the pipeline is described as a BCO in that file, and the BCO can be parsed once inside the FDA.
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?''' If the sponsor already has a submission in-house and under review, they should directly contact the Regulatory Project Manager (RPM) assigned to that submission for assistance and guidance related to BioCompute Object submissions.
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?''' If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.

== Publications ==
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].

FAQs

2024-05-14T16:48:54Z

ChinweokeO:

'''Go back to [[Main Page|BioCompute Objects]].'''

== General ==
1. '''How can I build a BioCompute Object (BCO)?'''

You have several options for building a BCO. You can use the standalone "builder" tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.

2. '''What are the minimum requirements for conformance with the BioCompute standard?'''

The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.

3. '''How can I ensure my submission validates against the BioCompute schema?'''

Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].

4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].

5. '''Can you provide an example of a completed BioCompute Object (BCO)?'''

Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.

6. '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''

Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.

7. '''How can a third-party access URIs in a BCO?'''

URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all.

8. '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''

If the sponsor already has a submission in-house and under review, they should directly contact the Regulatory Project Manager (RPM) assigned to that submission for assistance and guidance related to BioCompute Object submissions.

9. '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''

If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.

10. '''What is a SHA1 Checksum?'''

A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.

11. '''How do I sign in with an ORCID/What is an ORCID?'''

[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID, create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.

== Pipeline Questions ==

1. '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''

The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).

2. '''What is the nf-core plugin and how can I test it?'''

The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:

* Ensure you have the latest version of the plugin installed.

* Add the following code snippets to your Nextflow configuration file:

plugins {

id 'nf-prov'

}

prov.enabled = true

prov {

formats {

bco {

file = 'bco.json'

overwrite = true

}

}

}

These settings will enable the BCO format and specify the output file as "bco.json". Ensure you include these snippets in your configuration file to activate the BCO format.

For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]

== Inputs and Outputs ==

1. '''What is the relationship and difference between input_list in description_domain and input_subdomain? Does input_subdomain contain all the input files of all the pipeline steps?'''

Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.

2. '''What is the relationship and difference between output_list in description_domain and output_subdomain? Does output_subdomain contain all the output files of all the pipeline steps?'''

The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.

3. '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''

Yes they are, the timestamp is used for creation in those cases.

4. '''Can a script from the execution domain also be considered an input?'''

This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.

== Extensions ==

1. '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''

Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.

2. '''How can BCOs be used for knowledgebases?'''

Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.

BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.

The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.

== Prerequisites ==

1. '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''

Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.

== Knowledgebases ==

1. '''Can BCOs be used for curating databases?'''

Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.

Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.

BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.

The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.

== Saving and Publishing a BCO ==

1. '''Why is my BCO not saved after clicking '''SAVE'''?'''

The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.

2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''

A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.

3. '''How should I submit a BCO with a regulatory submission?'''

A BCO file can be saved as a plain text (".txt") document and submitted with a regulatory submission. You can inform the reviewer that the pipeline is described as a BCO in that file, and the BCO can be parsed once inside the FDA.

== BCO Validation and Error messages ==

The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.

1. '''"[description_domain][pipeline_steps][0][step_number]": "'1' is not of type 'integer'"'''

The '''step_number''' in the BCO JSON needs to be an INTEGER.

This means it can not be in quotes like this:
''' "step_number": "1",'''
Instead, it must be represented like this:
''' "step_number": 1,'''

You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.

== Publications ==
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].

BioCompute Conference and Workshop

2024-05-09T17:32:18Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:10 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Hadley King'''
<small>Research Scientist, HIVE Lab, George Washington University</small>
|BioCompute Portal, BioCompute Database, and User Database: Why so many?
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Virginia Hussong.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Virginia Hussong</div></big>
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:HadleyKing.png|alt=Headshot for Hadley King|center|thumb|200x200px]]<big><div style="text-align: center;">Hadley King</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|[[File:Julia Maritz.jpg|none|thumb|204x204px]]<big><div style="text-align: center;">Julia Maritz</div></big>
|}

== <big>Use Case Collection Form</big>==
<big>Please take a moment to fill out our use case collection form here: https://docs.google.com/forms/d/e/1FAIpQLSfS5E-cpPMvIdEHVqPiZnmcpsH5JetMsBAY2vnsemRWeDj5uw/viewform </big>

==<big>Contact Us</big>==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-07T20:51:39Z

ChinweokeO: /* Use Case Collection Form */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:10 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Virginia Hussong.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Virginia Hussong</div></big>
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|[[File:Julia Maritz.jpg|none|thumb|204x204px]]<big><div style="text-align: center;">Julia Maritz</div></big>
|}

== <big>Use Case Collection Form</big>==
<big>Please take a moment to fill out our use case collection form here: https://docs.google.com/forms/d/e/1FAIpQLSfS5E-cpPMvIdEHVqPiZnmcpsH5JetMsBAY2vnsemRWeDj5uw/viewform </big>

==<big>Contact Us</big>==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-07T20:50:42Z

ChinweokeO: /* Use Case Collection Form */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:10 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Virginia Hussong.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Virginia Hussong</div></big>
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|[[File:Julia Maritz.jpg|none|thumb|204x204px]]<big><div style="text-align: center;">Julia Maritz</div></big>
|}

== <big>Use Case Collection Form</big>==
<big>Please take a moment to fill out our use case collection form here:</big> https://docs.google.com/forms/d/e/1FAIpQLSfS5E-cpPMvIdEHVqPiZnmcpsH5JetMsBAY2vnsemRWeDj5uw/viewform

==<big>Contact Us</big>==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-07T20:50:14Z

ChinweokeO:

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:10 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Virginia Hussong.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Virginia Hussong</div></big>
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|[[File:Julia Maritz.jpg|none|thumb|204x204px]]<big><div style="text-align: center;">Julia Maritz</div></big>
|}

== <big>Use Case Collection Form</big>==
<big>Please take a moment to fill out our use case collection form here</big>

==<big>Contact Us</big>==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-05T21:16:14Z

ChinweokeO: /* Schedule */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:10 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Virginia Hussong.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Virginia Hussong</div></big>
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|[[File:Julia Maritz.jpg|none|thumb|204x204px]]<big><div style="text-align: center;">Julia Maritz</div></big>
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-05T20:08:35Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Virginia Hussong.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Virginia Hussong</div></big>
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|[[File:Julia Maritz.jpg|none|thumb|204x204px]]<big><div style="text-align: center;">Julia Maritz</div></big>
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

File:Julia Maritz.jpg

2024-05-05T20:08:00Z

ChinweokeO:

Julia Maritz

BioCompute Conference and Workshop

2024-05-05T20:06:52Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Virginia Hussong.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Virginia Hussong</div></big>
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-05T20:05:32Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|[[File:Virginia Hussong.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Virginia Hussong</div></big>
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

File:Virginia Hussong.jpg

2024-05-05T20:04:49Z

ChinweokeO:

Virginia Hussong

BioCompute Conference and Workshop

2024-05-05T20:03:38Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-05T20:03:13Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|222x222px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|[[File:Mark Walderhaug.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Mark Walderhaug</div></big>
|
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

File:Mark Walderhaug.jpg

2024-05-05T20:01:47Z

ChinweokeO:

Mark Walderhaug

BioCompute Conference and Workshop

2024-05-05T19:52:41Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|thumb|203x203px|center]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|222x222px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|
|
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-05T19:52:15Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|254x254px|none]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|222x222px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|
|
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-05T19:51:41Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|200x200px|]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|[[File:Soiland-Reyes.jpg|none|thumb|222x222px]]<big><div style="text-align: center;">Stian Soiland-Reyes</div></big>
|
|
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

File:Soiland-Reyes.jpg

2024-05-05T19:49:51Z

ChinweokeO:

Stian Soiland-Reyes

BioCompute Conference and Workshop

2024-05-05T18:20:58Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|-
|[[File:Guangzhi Sun.jpg|thumb|337x337px|center]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|
|
|
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-05T18:18:04Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15 - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30 - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40 - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55 - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|-
|[[File:Guangzhi Sun.jpg|none|thumb|200x200px]]<big><div style="text-align: center;">Guangzhi Sun</div></big>
|
|
|
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

File:Guangzhi Sun.jpg

2024-05-05T18:16:12Z

ChinweokeO:

Associate Researcher, China National Institute of Standardization (CNIS), ISO

BioCompute Conference and Workshop

2024-05-03T21:05:11Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15PM - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30PM - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40PM - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55PM - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|center]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-03T21:04:36Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15PM - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30PM - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40PM - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55PM - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px|none]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-03T21:04:09Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15PM - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30PM - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40PM - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55PM - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|199x199px]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-03T21:03:40Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15PM - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30PM - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40PM - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55PM - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|211x211px]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-05-03T21:03:08Z

ChinweokeO: /* Confirmed Presenters */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00 - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 9:45
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!9:45 - 10:00AM
! colspan="2" |''Break''
|-
!10:00 - 10:55AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:00 - 10:15
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:15 - 10:30
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:30 - 10:45
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|10:45 - 10:55
| colspan="2" |''Discussion''
|-
!10:55 - 11:10AM
! colspan="2" |''Break and poster review''
|-
!11:10 - 12:05PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:10 - 11:25
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:25 - 11:40
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:40 - 11:55
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:55 - 12:05
| colspan="2" |''Discussion''
|-
!
!12:05 - 1:10PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="18" |Afternoon
Session
!1:40 - 4:30PM
! colspan="2" |<big>Technical, Administrative, and Usability Session</big>
|-
|1:10 - 1:25
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:25 - 1:40
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:40 - 1:55
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!1:55 - 2:10PM
! colspan="2" |''Break and Poster review''
|-
|2:10 - 2:25
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:25 - 2:40
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Steph Singleton'''
<small>Bioinformatics Scientist, Technical Project Manager, Essential Software Inc.</small>
|Capturing Machine Learning Pipelines via BioCompute Objects
|-
!3:15PM - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30PM - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40PM - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55PM - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|[[File:Steph photo argos2.jpeg|alt=Headshot for Steph Singleton|thumb|220x220px]]<big><div style="text-align: center;">Stephanie Singleton</div></big>
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-04-30T14:15:27Z

ChinweokeO: /* Schedule */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00AM - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 10:00
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!10:00AM - 10:15AM
! colspan="2" |''Break''
|-
!10:15AM - 11:10AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:15 - 10:30
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:30 - 10:45
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:45 - 11:00
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|11:00am - 11:10am
| colspan="2" |''Discussion''
|-
!11:10AM - 11:25AM
! colspan="2" |''Break and poster review''
|-
!11:25AM - 12:20PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:25 - 11:40
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:40 - 11:55
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:55 - 12:10
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|12:10 - 12:20
| colspan="2" |''Discussion''
|-
!
!12:20PM - 1:25PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="17" |Afternoon
Session
!1:25PM - 4:30PM
! colspan="2" |<big>Progress Towards Usability</big>
|-
|1:25 - 1:40
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:40 - 1:55
|'''Virginia Hussong'''
<small>Miscellaneous Administration and Program, FDA</small>
|Forthcoming Guidance for BCO Submission
|-
|1:55 - 2:10
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!2:10PM - 2:25PM
! colspan="2" |''Break and Poster review''
|-
|2:25 - 2:40
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
!3:15PM - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30PM - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40PM - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55PM - 5:00PM
! colspan="2" |Closing
''Mark Walderhaug and Raja Mazumder''
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-04-24T16:59:26Z

ChinweokeO: /* Schedule */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00AM - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 10:00
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!10:00AM - 10:15AM
! colspan="2" |''Break''
|-
!10:15AM - 11:10AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:15 - 10:30
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:30 - 10:45
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:45 - 11:00
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|11:00am - 11:10am
| colspan="2" |''Discussion''
|-
!11:10AM - 11:25AM
! colspan="2" |''Break and poster review''
|-
!11:25AM - 12:20PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:25 - 11:40
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:40 - 11:55
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:55 - 12:10
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|12:10 - 12:20
| colspan="2" |''Discussion''
|-
!
!12:20PM - 1:25PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="17" |Afternoon
Session
!1:25PM - 4:30PM
! colspan="2" |<big>Progress Towards Usability</big>
|-
|1:25 - 1:40
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:40 - 1:55
|Regualtory Advisory Board representative
|Forthcoming Guidance for BCO Submission
|-
|1:55 - 2:10
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!2:10PM - 2:25PM
! colspan="2" |''Break and Poster review''
|-
|2:25 - 2:40
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:40 - 3:00
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:00 - 3:15
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
!3:15PM - 3:30PM
! colspan="2" |''Break and Poster review''
|-
|3:30 - 3:45
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:45 - 4:00
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:00 - 4:15
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:15 - 4:30
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:30PM - 4:40PM
! colspan="2" |''Break and Poster review''
|-
!4:40PM - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:40 - 4:55
|Chosen speakers
|Poster lightning talks
|-
!4:55PM - 5:00PM
! colspan="2" |Closing
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-04-24T16:19:44Z

ChinweokeO: /* Schedule */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
! rowspan="17" |Morning
Session
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00AM - 10:00AM
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00 - 9:15
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15 - 9:30
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30 - 10:00
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Plenary Address
|-
!10:00AM - 10:15AM
! colspan="2" |''Break''
|-
!10:15AM - 11:10AM
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|10:15 - 10:30
|'''Vahan Simonyan'''
<small>CSO, Embleema, DNA HIVE</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|10:30 - 10:45
|'''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
|A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|10:45 - 11:00
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|11:00am - 11:10am
| colspan="2" |''Discussion''
|-
!11:10AM - 11:25AM
! colspan="2" |''Break and poster review''
|-
!11:25AM - 12:20PM
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|11:25 - 11:40
| '''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Workflows
|-
|11:40 - 11:55
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:55 - 12:10
| '''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
| Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|12:10 - 12:20
| colspan="2" |''Discussion''
|-
!
!12:20PM - 1:30PM
! colspan="2" |''Lunch & Poster Session''
|-
! rowspan="17" |Afternoon
Session
!1:30PM - 4:35PM
! colspan="2" |<big>Progress Towards Usability</big>
|-
|1:30 - 1:45
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:45 - 2:00
|Regualtory Advisory Board representative
|Forthcoming Guidance for BCO Submission
|-
|2:00 - 2:15
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!2:15PM - 3:20PM
! colspan="2" |''Break and Poster review''
|-
|2:30 - 2:45
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:45 - 3:05
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:05 - 3:20
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
!3:20PM - 3:35PM
! colspan="2" |''Break and Poster review''
|-
|3:35 - 3:50
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:50 - 4:05
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:05 - 4:20
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:20 - 4:35
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:35PM - 4:45PM
! colspan="2" |''Break and Poster review''
|-
!4:45PM - 5:00PM
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:45 - 5:00
|Chosen speakers
|Poster lightning talks
|-
!5:00PM
! colspan="2" |Closing
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-04-23T21:19:50Z

ChinweokeO: /* Getting there */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00am - 10:00am
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00am - 9:15am
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15am - 9:30am
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30am - 9:45am
|'''Vahan Simonyan'''
<small>CSO, Embleema</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|9:45am - 10:15am
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Vision
|-
!10:15am - 10:30am
! colspan="2" |''Break''
|-
!10:30am - 11:15am
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|10:30am - 10:45am
|'''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Standards
|-
|10:45am - 11:00am
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:00am - 11:15am
|'''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
|Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:15am - 11:25am
| colspan="2" |''Discussion''
|-
!11:25am - 11:35am
! colspan="2" |''Break and poster review''
|-
!11:35am - 12:30am
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|11:35am - 11:50am
| UNCONFIRMED
|TBD
|-
|11:50am - 12:05pm
| '''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
| A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|12:05pm - 12:20pm
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|12:20pm - 12:30pm
| colspan="2" |''Discussion''
|-
!12:30pm - 1:30pm
! colspan="2" |''Lunch & Poster Session''
|-
!1:30pm - 4:35pm
! colspan="2" |<big>Progress Towards Usability</big>
|-
|1:30pm - 1:45pm
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:45pm - 2:00pm
|Regualtory Advisory Board representative
|Forthcoming Guidance for BCO Submission
|-
|2:00pm - 2:15pm
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!2:15pm - 2:30pm
! colspan="2" |''Break and Poster review''
|-
|2:30pm - 2:45pm
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:45pm - 3:05pm
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:05pm - 3:20pm
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
!3:20pm - 3:35pm
! colspan="2" |''Break and Poster review''
|-
|3:35pm - 3:50pm
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:50pm - 4:05pm
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:05pm - 4:20pm
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:20pm - 4:35pm
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:35pm - 4:45pm
! colspan="2" |''Break and Poster review''
|-
!4:45pm - 5:00pm
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:45pm - 5:00pm
|Chosen speakers
|Poster lightning talks
|-
!5:00pm
! colspan="2" |Closing
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-04-23T19:23:10Z

ChinweokeO: /* Accommodation */

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the activities planned for the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
<big>If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.</big>

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00am - 10:00am
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00am - 9:15am
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15am - 9:30am
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30am - 9:45am
|'''Vahan Simonyan'''
<small>CSO, Embleema</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|9:45am - 10:15am
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Vision
|-
!10:15am - 10:30am
! colspan="2" |''Break''
|-
!10:30am - 11:15am
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|10:30am - 10:45am
|'''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Standards
|-
|10:45am - 11:00am
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:00am - 11:15am
|'''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
|Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:15am - 11:25am
| colspan="2" |''Discussion''
|-
!11:25am - 11:35am
! colspan="2" |''Break and poster review''
|-
!11:35am - 12:30am
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|11:35am - 11:50am
| UNCONFIRMED
|TBD
|-
|11:50am - 12:05pm
| '''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
| A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|12:05pm - 12:20pm
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|12:20pm - 12:30pm
| colspan="2" |''Discussion''
|-
!12:30pm - 1:30pm
! colspan="2" |''Lunch & Poster Session''
|-
!1:30pm - 4:35pm
! colspan="2" |<big>Progress Towards Usability</big>
|-
|1:30pm - 1:45pm
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:45pm - 2:00pm
|Regualtory Advisory Board representative
|Forthcoming Guidance for BCO Submission
|-
|2:00pm - 2:15pm
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!2:15pm - 2:30pm
! colspan="2" |''Break and Poster review''
|-
|2:30pm - 2:45pm
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:45pm - 3:05pm
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:05pm - 3:20pm
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
!3:20pm - 3:35pm
! colspan="2" |''Break and Poster review''
|-
|3:35pm - 3:50pm
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:50pm - 4:05pm
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:05pm - 4:20pm
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:20pm - 4:35pm
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:35pm - 4:45pm
! colspan="2" |''Break and Poster review''
|-
!4:45pm - 5:00pm
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:45pm - 5:00pm
|Chosen speakers
|Poster lightning talks
|-
!5:00pm
! colspan="2" |Closing
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>

BioCompute Conference and Workshop

2024-04-23T15:36:05Z

ChinweokeO:

'''<big>2024 BioCompute Conference and Workshop</big>'''

''<big>This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s "Portal" for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. This conference will have perspectives from both FDA and industry around the use of BioCompute in regulatory submissions, challenges for implementation, and tools designed to work with the standard. Join us for an in-depth discussion of BCO standards and an opportunity to view other projects during our poster session.</big>''

<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>

<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>

<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>

==== <big>'''<u>Getting there</u>'''</big> ====
<big>We encourage all attendees to arrive around 8:30 AM, thirty minutes prior to the start of the event at 9:00 AM, to ensure they have enough time to settle in and make the most of the activities planned for the day.</big>

'''<big>By Car</big>'''

<big>Enter "FDA Building 1" in Google Maps, then follow NW Loop Rd to the closest visitor parking, once reach the T-section turn right onto Michelson Rd to vehicle security screening before parking on the White Oak campus. FDA circulator shuttles are available between visitor parking and Building 1. Refer to the [https://www.fda.gov/about-fda/visitor-information/visitor-parking-and-campus-map FDA] website for the campus map.</big>

<big>'''By metro'''
'''Public buses:'''</big>
* <big>Ride On Bus [https://www.montgomerycountymd.gov/DOT-Transit/routesandschedules/allroutes/route022.html Route 22] - stops at the Silver Spring (Red line) Metro station</big>
* <big>BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station</big>
* <big>Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations</big>
* <big>Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
* <big>Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station</big>
'''<big>FDA shuttle to metro:</big>'''
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-college-park-metro-station College Park Metro] (Green line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-glenmont-metro-station Glenmont Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-medical-center-metro-station Medical Center Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-shady-grove-metro-station Shady Grove Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-stop-location-silver-spring-metro-station Silver Spring Metro] (Red line)</big>
* <big>[https://www.fda.gov/about-fda/white-oak-campus-information/white-oak-shuttle-bus-location-twinbrook-metro-station Twinbrook Metro] (Red line)</big>
* More FDA shuttle info can be found [https://www.fda.gov/media/92208/download?attachment here]

<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>

=== <u>Accommodation</u> ===
If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: [https://www.foundationforpn.org/wp-content/uploads/2016/04/Hotels-by-the-FDA-White-Oak.pdf Hotels by the FDA White Oak Campus]. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.

== <big>Abstract</big> ==
<big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for precisely yet adaptable describing workflows. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big>

<big>As the field evolves, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big>

<big>The [https://www.biocomputeobject.org/ BioCompute Portal], the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. In addition, the FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. All of the most up-to-date information about BioCompute will be introduced at the workshop and followed by a roundtable discussion to further improve the applicability of BioCompute from the FDA point of view and industry-wise.</big>

=== <big><u>Organization Committee</u></big> ===
<big>Jonathon Kenney (GWU/Chair); Raja Mazumder (GWU); Mark Walderhaug (FDA); Luis Santana-Quintero(FDA); Charles Hadley King (GWU); Omar Serang (DNAnexus); Sam Westreich (DNAnexus); Dennis A. Dean, II (Velsera); Phil Webster (Velsera); Kostis Karagiannis (Moderna)</big>

== <big>Workshop Topics</big> ==
* <big>Updates and future for BioCompute</big>
* <big>Need for BCO at FDA</big>
* <big>Considerations for Adoption in Industry</big>
* <big>Progress Towards Usability</big>
* <big>BCODB and Portal's use at the FDA</big>
* <big>BCO platform interoperability</big>
* <big>Exemplar workflows and real-world applications</big>
* <big>BCO-Nextflow</big>
* <big>Potential AI/ML-related implementations</big>
* <big>FAQ session & Roundtable discussion</big>

== <big>Poster Session</big> ==
<big>Participants are encouraged to submit a poster abstract by April 15th, 11:59 PM (EDT). Posters should describe a computational pipeline or topic related to BioCompute. Up to 5 posters will have their workflows converted into a BCO by the BCO team and published in the BCO Portal, and will be offered a 5-minute lightning talk at the end of the conference. All posters must be printed before the workshop and set up at the start of the event.</big>

<big>'''Abstract'''</big>: <big>Any computational workflow of interest, or topic related to BCOs</big>

<big>'''Poster Content''': Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.</big>

<big>'''Size''': poster sizes can be up to 4' tall x 6' wide.</big>

<big>'''Submission Portal''': click [https://docs.biocomputeobject.org/submit/ here].</big>

== <big>Schedule</big> ==
{| class="wikitable"
!<big>Time</big>
!<big>Speaker</big>
!<big>Content</big>
|-
!9:00am - 10:00am
! colspan="2" |<big>Introduction and Future for BioCompute</big>
|-
|9:00am - 9:15am
|'''Jonathon Keeney'''
<small>Research Assistant Professor, George Washington University</small>
|Welcome and Introduction
|-
|9:15am - 9:30am
|'''Raja Mazumder'''
<small>Professor, George Washington University</small>
|Vision and Future of BioCompute
|-
|9:30am - 9:45am
|'''Vahan Simonyan'''
<small>CSO, Embleema</small>
|BioCompute Vision from an FDA-Industry Perspective
|-
|9:45am - 10:15am
| '''Peter Marks'''
<small>Director, CBER, FDA</small>
|Vision
|-
!10:15am - 10:30am
! colspan="2" |''Break''
|-
!10:30am - 11:15am
! colspan="2" |<big>Need for BCO at FDA</big>
|-
|10:30am - 10:45am
|'''Mark Walderhaug'''
<small>Associate Director for Risk Assessment, CBER, FDA</small>
|BioCompute Objects and Standards
|-
|10:45am - 11:00am
|'''Luis Santana-Quintero'''
<small>HIVE lead, CBER, FDA</small>
|Computational Reviews at CBER
|-
|11:00am - 11:15am
|'''Eric Donaldson'''
<small>Clinical Virology Reviewer</small>
|Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review
|-
|11:15am - 11:25am
| colspan="2" |''Discussion''
|-
!11:25am - 11:35am
! colspan="2" |''Break and poster review''
|-
!11:35am - 12:30am
! colspan="2" |<big>Considerations for Adoption in Industry</big>
|-
|11:35am - 11:50am
| UNCONFIRMED
|TBD
|-
|11:50am - 12:05pm
| '''Jun Luo'''
<small>Data Scientist, Novo Nordisk</small>
| A Computational Framework for end-to-end Clinical Omics Analysis: Single Cell Mechanism of action study in chronic diseases
|-
|12:05pm - 12:20pm
|'''Julia Maritz'''
<small>Senior Scientist, Merck</small>
|Applications of BioCompute Objects for Viral Metagenomics Analysis
|-
|12:20pm - 12:30pm
| colspan="2" |''Discussion''
|-
!12:30pm - 1:30pm
! colspan="2" |''Lunch & Poster Session''
|-
!1:30pm - 4:35pm
! colspan="2" |<big>Progress Towards Usability</big>
|-
|1:30pm - 1:45pm
|'''Susan Gregurick'''
<small>Director of Data Science, NIH</small>
|AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future
|-
|1:45pm - 2:00pm
|Regualtory Advisory Board representative
|Forthcoming Guidance for BCO Submission
|-
|2:00pm - 2:15pm
|'''Guangzhi Sun'''
<small>Associate Researcher, China National Institute of Standardization (CNIS), ISO</small>
|Extending BCO specification into a Generic Metamodel for Computable Data
|-
!2:15pm - 2:30pm
! colspan="2" |''Break and Poster review''
|-
|2:30pm - 2:45pm
|'''Jonas Almeida'''
<small>Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI</small>
|Functionalization of Biocompute Objects using Generative AI
|-
|2:45pm - 3:05pm
|'''Dennis Dean'''
<small>Director of Translational Sciences, Velsera</small>
|Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case
|-
|3:05pm - 3:20pm
|'''Sam Westreich'''
<small>Sr. Scientific Program Manager, DNAnexus</small>
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
!3:20pm - 3:35pm
! colspan="2" |''Break and Poster review''
|-
|3:35pm - 3:50pm
|'''Stian Soiland-Reyes and Meznah Aloqalaa'''
<small>Senior Lecturer, University of Manchester/Ph.D. Student</small>
|BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows
|-
|3:50pm - 4:05pm
|'''Ben Sherman'''
<small>Developer, Seqera Labs</small>
|Generating BioCompute Objects for Nextflow Pipelines
|-
|4:05pm - 4:20pm
|'''Konstantinos Krampis'''
<small>Associate Professor of Biology and Computer Science, CUNY</small>
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
|4:20pm - 4:35pm
|'''Sean Kim'''
<small>Bioinformatics Specialist, George Washington University</small>
|Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers
|-
!4:35pm - 4:45pm
! colspan="2" |''Break and Poster review''
|-
!4:45pm - 5:00pm
! colspan="2" |<big>Lightning talk and closing</big>
|-
|4:45pm - 5:00pm
|Chosen speakers
|Poster lightning talks
|-
!5:00pm
! colspan="2" |Closing
|}

== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Peter Marks.png|none|thumb|245x245px]]<big><div style="text-align: center;">Peter Marks</div></big>
|[[File:Susan K. Gregurick.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Susan K. Gregurick</div></big>
|[[File:Mazumder, Raja.jpeg.jpg|none|thumb|245x245px]]<big><div style="text-align: center;">Raja Mazumder</div></big>
|[[File:Jonas Almeida.png|center|thumb|241x241px]]<big><div style="text-align: center;">Jonas Almeida</div></big>
|[[File:Jun Luo.png|none|thumb|240x240px]]<big><div style="text-align: center;">Jun Luo</div></big>
|-
|[[File:Vahan Simonyan.png|none|thumb|204x204px]] <big><div style="text-align: center;">Vahan Simonyan</div></big>
|[[File:Sam Westreich.jpg|thumb|204x204px|none]] <big><div style="text-align: center;">[https://www.linkedin.com/in/sam-westreich/ Sam Westreich]</div></big>
|[[File:Konstantinos Krampis.jpg|thumb|none]] <big><div style="text-align: center;">Konstantinos Krampis</div></big>
|[[File:Image001.png|thumb|200x200px|center]] <big><div style="text-align: center;">Eric Donaldson</div></big>
|[[File:Dennis Dean.png|center|thumb|200x200px]] <big><div style="text-align: center;">Dennis A. Dean, II</div></big>
|-
|[[File:Keeney Jonathon 5309 MOD.jpg|none|thumb|203x203px]]<big><div style="text-align: center;">[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney]</div></big>
|[[File:Luis.jpg|center|thumb|200x200px]] <big><div style="text-align: center;">Luis Santana-Quintero</div></big>
|[[File:Ben Sherman.png|none|thumb|200x200px]] <big><div style="text-align: center;">Ben Sherman</div></big>
|[[File:Sean Kim.png|none|thumb|222x222px]]<big><div style="text-align: center;">Sean Kim</div></big>
|
|}

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries about BioCompute, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] or refer to our [https://wiki.biocomputeobject.org/index.php?title=FAQs# FAQs]</big>