BCOeditor Wiki - User contributions [en]

BioCompute Conference and Workshop

2024-02-06T15:31:52Z

Hadleyking:

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

''<big>This workshop provides an opportunity to learn about the most up-to-date updates of BioCompute Objects and interoperability between 3 platforms that host BioCompute Objects (BCO). It will also cover BCODB and Portal's use at the FDA, real-world applications, and potential AL/ML-related BCO implementations. We encourage everyone to attend in person for hands-on experience, discussion and 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>'''Getting there'''</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>

== <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>Organization Committee</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>All participants are encouraged to submit a poster by April 5th and the top 5 posters that best match BioCompute missions will have the opportunity to do a lightning talk at the end of the day. All posters must be printed before the workshop and set up the posters before the workshop starts.</big>

<big>Content: Any chosen workflow that can engage BCO. More detail coming.</big>

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

<big>Submission: Submission portal coming soon.</big>

== <big>Schedule</big> ==
{| class="wikitable"
!Time
!Speaker
!Content/Title
|-
!9:00 - 10:05
! colspan="2" |Introduction and Future for BioCompute
|-
|9:00 - 9:10
|Raja Mazumder
|Introduction
|-
|9:10 - 9:25
|Jonathon Keeney
|Future of BioCompute
|-
|9:25 - 10:00
| Plenary Speaker
|Vision
|-
!10:00 - 11:00
! colspan="2" |Need for BCO at FDA
|-
|10:00 - 10:20
|Mark Walderhaug
|Why BCO/RAB updates
|-
|10:20 - 10:35
|Luis Santana-Quintero
|Computational Reviews at CBER
|-
|10:35 - 10:50
|Arifa Khan (UNCONFIRMED)
|Perspectives from a Reviewer
|-
!10:50 - 11:00
! colspan="2" |Discussion
|-
!11:00 - 11:20
! colspan="2" |''Break and poster review''
|-
!11:20 - 12:15
! colspan="2" |Considerations for Adoption in Industry
|-
|11:20 - 11:35
| Konstantinos Karagiannis
|Challenges to adoption at Moderna
|-
|11:35 - 11:50
| Vanessa Sarathy
| Challenges to adoption at Merck
|-
|11:50 - 12:05
|Nuria Guimera
|Challenges to adoption at J&J
|-
|12:05 - 12:15
|Vahan Simonyan
|BioCompute vision from an FDA-Industry perspective
|-
!12:15 - 1:15
! colspan="2" |''Lunch & Poster Session''
|-
!1:15 - 4:10
! colspan="2" |Progress Towards Usability
|-
|1:15 - 1:30
|Dennis Dean
|Velsera
|-
|1:30 - 1:45
|Sam Westreich
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
!1:45 - 2:00
! colspan="2" |''Break and Poster review''
|-
|2:00 - 2:15
|Stian Soiland-Reyes
|BCO-RO
|-
|2:15 - 2:30
|Nextflow/Seqera Representative
|Nextflow-BCO
|-
|2:30 - 2:45
|Konstantinos Krampis
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
!2:45 - 3:05
! colspan="2" |''Break and Poster review''
|-
|3:05 - 3:20
|Denise Warzel
|ISO publication
|-
|3:20 - 3:35
|Elaine Thompson
|BCO-CDISC: An emerging role for BioCompute: CDISC Standards for Cell and Gene Therapy Product (CGTP) Monitoring.
|-
|3:35 - 3:50
|RAB representative
|Forthcoming Guidance for BCO Submission
|-
!3:50 - 4:05
! colspan="2" |''Break and Poster review''
|-
!4:05 - 5:00
! colspan="2" |Lightning talk and closing
|-
|4:05 - 4:45
|Chosen speakers
|Poster lightning talks
|-
!4:45 - 5:00
! colspan="2" |Closing
|}
== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Sam Westreich.jpg|thumb|204x204px|none]]<big>[https://www.linkedin.com/in/sam-westreich/ Sam Westreich] - DNAnexus</big>
|[[File:Konstantinos Krampis.jpg|thumb|none]]<big>Konstantinos Krampis</big>
|[[File:Elaine Thompson.jpg|thumb|200x200px|none]]<big>Elaine E. Thompson, Ph.D.</big>
|}
<big>Dennis A. Dean, II - Velsera</big>

<big>[https://www.linkedin.com/in/phillipjwebster/ Phil Webster]- Velsera</big>

<big>[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney] - The George Washington University (GWU)</big>

<big>[https://www.linkedin.com/in/charles-hadley-king-942693a8/ Charles Hadley King] - The George Washington University (GWU)</big>

<big>[https://www.linkedin.com/in/omarserang/ Omar Serang] - DNAnexus</big>

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] </big>

BioCompute Conference and Workshop

2024-02-06T15:30:10Z

Hadleyking:

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

''<big>This workshop provides an opportunity to learn about the most up-to-date updates of BioCompute Objects and interoperability between 3 platforms that host BioCompute Objects (BCO). It will also cover BCODB and Portal's use at the FDA, real-world applications, and potential AL/ML-related BCO implementations. We encourage everyone to attend in person for hands-on experience, discussion and 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>'''Getting there'''</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>

== <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>Organization Committee</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>All participants are encouraged to submit a poster by April 5th and the top 5 posters that best match BioCompute missions will have the opportunity to do a lightning talk at the end of the day. All posters must be printed before the workshop and set up the posters before the workshop starts.</big>

<big>Content: Any chosen workflow that can engage BCO. More detail coming.</big>

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

<big>Submission: Submission portal coming soon.</big>

== <big>Schedule</big> ==
{| class="wikitable"
!Time
!Speaker
!Content/Title
|-
!9:00 - 10:05
! colspan="2" |Introduction and Future for BioCompute
|-
|9:00 - 9:10
|Raja Mazumder
|Introduction
|-
|9:10 - 9:25
|Jonathon Keeney
|Future of BioCompute
|-
|9:25 - 10:00
| Plenary Speaker
|Vision
|-
!10:00 - 11:00
! colspan="2" |Need for BCO at FDA
|-
|10:00 - 10:20
|Mark Walderhaug
|Why BCO/RAB updates
|-
|10:20 - 10:35
|Luis Santana-Quintero
|Computational Reviews at CBER
|-
|10:35 - 10:50
|Cinque Soto
|Perspectives from a Reviewer
|-
!10:50 - 11:00
! colspan="2" |Discussion
|-
!11:00 - 11:20
! colspan="2" |''Break and poster review''
|-
!11:20 - 12:15
! colspan="2" |Considerations for Adoption in Industry
|-
|11:20 - 11:35
| Konstantinos Karagiannis
|Challenges to adoption at Moderna
|-
|11:35 - 11:50
| Vanessa Sarathy
| Challenges to adoption at Merck
|-
|11:50 - 12:05
|Nuria Guimera
|Challenges to adoption at J&J
|-
|12:05 - 12:15
|Vahan Simonyan
|BioCompute vision from an FDA-Industry perspective
|-
!12:15 - 1:15
! colspan="2" |''Lunch & Poster Session''
|-
!1:15 - 4:10
! colspan="2" |Progress Towards Usability
|-
|1:15 - 1:30
|Dennis Dean
|Velsera
|-
|1:30 - 1:45
|Sam Westreich
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
!1:45 - 2:00
! colspan="2" |''Break and Poster review''
|-
|2:00 - 2:15
|Stian Soiland-Reyes
|BCO-RO
|-
|2:15 - 2:30
|Nextflow/Seqera Representative
|Nextflow-BCO
|-
|2:30 - 2:45
|Konstantinos Krampis
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
!2:45 - 3:05
! colspan="2" |''Break and Poster review''
|-
|3:05 - 3:20
|Denise Warzel
|ISO publication
|-
|3:20 - 3:35
|Elaine Thompson
|BCO-CDISC: An emerging role for BioCompute: CDISC Standards for Cell and Gene Therapy Product (CGTP) Monitoring.
|-
|3:35 - 3:50
|RAB representative
|Forthcoming Guidance for BCO Submission
|-
!3:50 - 4:05
! colspan="2" |''Break and Poster review''
|-
!4:05 - 5:00
! colspan="2" |Lightning talk and closing
|-
|4:05 - 4:45
|Chosen speakers
|Poster lightning talks
|-
!4:45 - 5:00
! colspan="2" |Closing
|}
== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Sam Westreich.jpg|thumb|204x204px|none]]<big>[https://www.linkedin.com/in/sam-westreich/ Sam Westreich] - DNAnexus</big>
|[[File:Konstantinos Krampis.jpg|thumb|none]]<big>Konstantinos Krampis</big>
|[[File:Elaine Thompson.jpg|thumb|200x200px|none]]<big>Elaine E. Thompson, Ph.D.</big>
|}
<big>Dennis A. Dean, II - Velsera</big>

<big>[https://www.linkedin.com/in/phillipjwebster/ Phil Webster]- Velsera</big>

<big>[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney] - The George Washington University (GWU)</big>

<big>[https://www.linkedin.com/in/charles-hadley-king-942693a8/ Charles Hadley King] - The George Washington University (GWU)</big>

<big>[https://www.linkedin.com/in/omarserang/ Omar Serang] - DNAnexus</big>

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] </big>

BioCompute Conference and Workshop

2024-02-06T15:29:12Z

Hadleyking:

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

''<big>This workshop provides an opportunity to learn about the most up-to-date updates of BioCompute Objects and interoperability between 3 platforms that host BioCompute Objects (BCO). It will also cover BCODB and Portal's use at the FDA, real-world applications, and potential AL/ML-related BCO implementations. We encourage everyone to attend in person for hands-on experience, discussion and 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>'''Getting there'''</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>

== <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>Organization Committee</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>All participants are encouraged to submit a poster by April 5th and the top 5 posters that best match BioCompute missions will have the opportunity to do a lightning talk at the end of the day. All posters must be printed before the workshop and set up the posters before the workshop starts.</big>

<big>Content: Any chosen workflow that can engage BCO. More detail coming.</big>

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

<big>Submission: Submission portal coming soon.</big>

== <big>Schedule</big> ==
{| class="wikitable"
!Time
!Speaker
!Content/Title
|-
!9:00 - 10:05
! colspan="2" |Introduction and Future for BioCompute
|-
|9:00 - 9:10
|Raja Mazumder
|Introduction
|-
|9:10 - 9:25
|Jonathon Keeney
|Future of BioCompute
|-
|9:25 - 10:00
| Plenary Speaker
|Vision
|-
!10:00 - 11:00
! colspan="2" |Need for BCO at FDA
|-
|10:00 - 10:20
|Mark Walderhaug
|Why BCO/RAB updates
|-
|10:20 - 10:35
|Luis Santana-Quintero
|Computational Reviews at CBER
|-
|10:35 - 10:50
|Cinque Soto
|Perspectives from a Reviewer
|-
!10:50 - 11:00
! colspan="2" |Discussion
|-
!11:00 - 11:20
! colspan="2" |''Break and poster review''
|-
!11:20 - 12:15
! colspan="2" |Considerations for Adoption in Industry
|-
|11:20 - 11:35
| Konstantinos Karagiannis
|Challenges to adoption at Moderna
|-
|11:35 - 11:50
| Vanessa Sarathy
| Challenges to adoption at Merck
|-
|11:50 - 12:05
|Nuria Guimera
|Challenges to adoption at J&J
|-
|12:05 - 12:15
|Vahan Simonyan
|BioCompute vision from an FDA-Industry perspective
|-
!12:15 - 1:15
! colspan="2" |''Lunch & Poster Session''
|-
!1:15 - 4:10
! colspan="2" |Progress Towards Usability
|-
|1:15 - 1:30
|Dennis Dean
|Velsera
|-
|1:30 - 1:45
|Sam Westreich
|DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor
|-
!1:45 - 2:00
! colspan="2" |''Break and Poster review''
|-
|2:00 - 2:15
|Stian Soiland-Reyes
|BCO-RO
|-
|2:15 - 2:30
|Nextflow/Seqera Representative
|Nextflow-BCO
|-
|2:30 - 2:45
|Konstantinos Krampis
|BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics
|-
!2:45 - 3:05
! colspan="2" |''Break and Poster review''
|-
|3:05 - 3:20
|Denise Warzel
|ISO publication
|-
|3:20 - 3:35
|Elaine Thompson
|BCO-CDISC: An emerging role for BioCompute: CDISC Standards for Cell and Gene Therapy Product (CGTP) Monitoring.
|-
|3:35 - 3:50
|RAB representative
|Forthcoming Guidance for BCO Submission
|-
!3:50 - 4:05
! colspan="2" |''Break and Poster review''
|-
!4:05 - 5:00
! colspan="2" |Lightning talk and closing
|-
|4:05 - 4:45
|Chosen speakers
|Poster lightning talks
|-
!4:45 - 5:00
! colspan="2" |Closing
|}
== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
|[[File:Sam Westreich.jpg|thumb|204x204px|none]]<big>[https://www.linkedin.com/in/sam-westreich/ Sam Westreich] - DNAnexus</big>
|[[File:Konstantinos Krampis.jpg|thumb|none]]<big>Konstantinos Krampis</big>
|[[File:Elaine Thompson.jpg|thumb|200x200px|none]]<big>Elaine E. Thompson, Ph.D.</big>
|}
<big>Dennis A. Dean, II - Velsera</big>

<big>[https://www.linkedin.com/in/phillipjwebster/ Phil Webster]- Velsera</big>

<big>[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney] - The George Washington University (GWU)</big>

<big>[https://www.linkedin.com/in/charles-hadley-king-942693a8/ Charles Hadley King] - The George Washington University (GWU)</big>

<big>[https://www.linkedin.com/in/omarserang/ Omar Serang] - DNAnexus</big>

== <big>Contact Us</big> ==
<big>For questions about registration or general inquiries, please go to [https://docs.biocomputeobject.org/contact/ Contact Us] </big>

File:GCC2022.poster.pdf

2022-08-10T16:04:25Z

Hadleyking:

Main Page

2022-07-28T19:50:48Z

Hadleyking:

== The BioCompute Standard ==

Because of the many different ways to organize data, a major goal of the BioCompute project is to build and maintain a formal standard through recognized, accredited standards setting organizations like the Institute for Electrical and Electronics Engineers (IEEE) and the International Standards Organization (ISO). A formal, consensus-based standard builds predictability and even more stability into the way in which bioinformatic methods are communicated.

The standard, officially known as 2791-2020, has two parts: the standards document and the schema, which is maintained in an open source repository:

* The current version of the standard can be found [here](https://standards.ieee.org/standard/2791-2020.html)**.
* The schema can be found [here](https://opensource.ieee.org/2791-object/ieee-2791-schema)**.

Since the base BioCompute schema is maintained as an open source repository, it can be cloned and integrated into an organization in unique ways, which allows organizations to build off of this schema to create dependent standards for specific applications. This is similar to the different versions of WiFi based on usage, such as the 802.11a standard for fast speed, but high cost and shorter range, or the 802.11b for slower top speed, but lower cost, etc. --- all of which are built on the 802.11 base standard. It can also be used to further extend the schema, such as for handling proprietary, internal content, while still being compatible with the base standard. The open source schema also enables individuals or organizations to suggest changes to be incorporated into future versions the standard.

=== Citation ===
This standard was originaly prepared by [The BioCompute Object working group](/BCO_Spec_V1.2.md#biocompute-object-consortium-members-bcoc) during preparation for the [2017 HTS Computational Standards for Regulatory Sciences Workshop](https://hive.biochemistry.gwu.edu/htscsrs/workshop_2017).

To reference the BCO standards, please use the following
citation inclusive of the DOI:

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](http://doi.org/10.5731/pdajpst.2016.006734)

=== Support, Community and Contributing ===

To suggest changes to [this repository](https://github.com/biocompute-objects/BCO_Specification) we welcome contributions as a [pull request](https://github.com/biocompute-objects/BCO_Specification/pulls) or [issue](https://github.com/biocompute-objects/BCO_Specification/issues) submission.

BCO_Specification is licensed under the [BSD 3-Clause "New" or "Revised" License](https://github.com/biocompute-objects/BCO_Specification/blob/main/LICENSE.md)

A permissive license similar to the BSD 2-Clause License, but with a 3rd clause that prohibits others from using the name of the project or its contributors to promote derived products without written consent.

=== Mailing List ===

As a subscriber to the BCO mailing list, you can post to it by sending a message tobiocomputels@hermes.gwu.edu (using the email address that is subscribed). This list is semi-automated and will send your message for review.

To subscribe or unsubscribe, please visit https://hermes.gwu.edu/cgi-bin/wa?A0=BIOCOMPUTELS and click `Subscribe` or `Unsubscribe` on the lower right. You can also unsubscribe from the list at any time by sending an email to listserv@hermes.gwu.edu, in which the body says: `unsubscribe biocomputels`

This repository is in support of [2791-2020](https://standards.ieee.org/standard/2791-2020.html) - IEEE Approved Draft Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication. Please also see our [OSF page](https://osf.io/h59uh/) or our [main page](https://biocomputeobject.org/)

Main Page

2022-07-28T19:48:31Z

Hadleyking:

== The BioCompute Standard ==

Because of the many different ways to organize data, a major goal of the BioCompute project is to build and maintain a formal standard through recognized, accredited standards setting organizations like the Institute for Electrical and Electronics Engineers (IEEE) and the International Standards Organization (ISO). A formal, consensus-based standard builds predictability and even more stability into the way in which bioinformatic methods are communicated.

The standard, officially known as 2791-2020, has two parts: the standards document and the schema, which is maintained in an open source repository:

* Bulleted list item
**The current version of the standard can be found [here](https://standards.ieee.org/standard/2791-2020.html)**.
* Bulleted list item
- **The schema can be found [here](https://opensource.ieee.org/2791-object/ieee-2791-schema)**.

Since the base BioCompute schema is maintained as an open source repository, it can be cloned and integrated into an organization in unique ways, which allows organizations to build off of this schema to create dependent standards for specific applications. This is similar to the different versions of WiFi based on usage, such as the 802.11a standard for fast speed, but high cost and shorter range, or the 802.11b for slower top speed, but lower cost, etc. --- all of which are built on the 802.11 base standard. It can also be used to further extend the schema, such as for handling proprietary, internal content, while still being compatible with the base standard. The open source schema also enables individuals or organizations to suggest changes to be incorporated into future versions the standard.

### Citation
This standard was originaly prepared by [The BioCompute Object working group](/BCO_Spec_V1.2.md#biocompute-object-consortium-members-bcoc) during preparation for the [2017 HTS Computational Standards for Regulatory Sciences Workshop](https://hive.biochemistry.gwu.edu/htscsrs/workshop_2017).

To reference the BCO standards, please use the following
citation inclusive of the DOI:

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](http://doi.org/10.5731/pdajpst.2016.006734)

## Support, Community and Contributing

To suggest changes to [this repository](https://github.com/biocompute-objects/BCO_Specification) we welcome contributions as a [pull request](https://github.com/biocompute-objects/BCO_Specification/pulls) or [issue](https://github.com/biocompute-objects/BCO_Specification/issues) submission.

BCO_Specification is licensed under the [BSD 3-Clause "New" or "Revised" License](https://github.com/biocompute-objects/BCO_Specification/blob/main/LICENSE.md)

>A permissive license similar to the BSD 2-Clause License, but with a 3rd clause that prohibits others from using the name of the project or its contributors to promote derived products without written consent.

## Mailing List

As a subscriber to the BCO mailing list, you can post to it by sending a message tobiocomputels@hermes.gwu.edu (using the email address that is subscribed). This list is semi-automated and will send your message for review.

To subscribe or unsubscribe, please visit https://hermes.gwu.edu/cgi-bin/wa?A0=BIOCOMPUTELS and click `Subscribe` or `Unsubscribe` on the lower right. You can also unsubscribe from the list at any time by sending an email to listserv@hermes.gwu.edu, in which the body says: `unsubscribe biocomputels`

This repository is in support of [2791-2020](https://standards.ieee.org/standard/2791-2020.html) - IEEE Approved Draft Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication. Please also see our [OSF page](https://osf.io/h59uh/) or our [main page](https://biocomputeobject.org/)

Main Page

2022-07-28T19:46:47Z

Hadleyking:

The BioCompute Standard

Because of the many different ways to organize data, a major goal of the BioCompute project is to build and maintain a formal standard through recognized, accredited standards setting organizations like the Institute for Electrical and Electronics Engineers (IEEE) and the International Standards Organization (ISO). A formal, consensus-based standard builds predictability and even more stability into the way in which bioinformatic methods are communicated.

The standard, officially known as 2791-2020, has two parts: the standards document and the schema, which is maintained in an open source repository:

- **The current version of the standard can be found [here](https://standards.ieee.org/standard/2791-2020.html)**.
- **The schema can be found [here](https://opensource.ieee.org/2791-object/ieee-2791-schema)**.

Since the base BioCompute schema is maintained as an open source repository, it can be cloned and integrated into an organization in unique ways, which allows organizations to build off of this schema to create dependent standards for specific applications. This is similar to the different versions of WiFi based on usage, such as the 802.11a standard for fast speed, but high cost and shorter range, or the 802.11b for slower top speed, but lower cost, etc. --- all of which are built on the 802.11 base standard. It can also be used to further extend the schema, such as for handling proprietary, internal content, while still being compatible with the base standard. The open source schema also enables individuals or organizations to suggest changes to be incorporated into future versions the standard.

### Citation
This standard was originaly prepared by [The BioCompute Object working group](/BCO_Spec_V1.2.md#biocompute-object-consortium-members-bcoc) during preparation for the [2017 HTS Computational Standards for Regulatory Sciences Workshop](https://hive.biochemistry.gwu.edu/htscsrs/workshop_2017).

To reference the BCO standards, please use the following
citation inclusive of the DOI:

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](http://doi.org/10.5731/pdajpst.2016.006734)

## Support, Community and Contributing

To suggest changes to [this repository](https://github.com/biocompute-objects/BCO_Specification) we welcome contributions as a [pull request](https://github.com/biocompute-objects/BCO_Specification/pulls) or [issue](https://github.com/biocompute-objects/BCO_Specification/issues) submission.

BCO_Specification is licensed under the [BSD 3-Clause "New" or "Revised" License](https://github.com/biocompute-objects/BCO_Specification/blob/main/LICENSE.md)

>A permissive license similar to the BSD 2-Clause License, but with a 3rd clause that prohibits others from using the name of the project or its contributors to promote derived products without written consent.

## Mailing List

As a subscriber to the BCO mailing list, you can post to it by sending a message tobiocomputels@hermes.gwu.edu (using the email address that is subscribed). This list is semi-automated and will send your message for review.

To subscribe or unsubscribe, please visit https://hermes.gwu.edu/cgi-bin/wa?A0=BIOCOMPUTELS and click `Subscribe` or `Unsubscribe` on the lower right. You can also unsubscribe from the list at any time by sending an email to listserv@hermes.gwu.edu, in which the body says: `unsubscribe biocomputels`

This repository is in support of [2791-2020](https://standards.ieee.org/standard/2791-2020.html) - IEEE Approved Draft Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication. Please also see our [OSF page](https://osf.io/h59uh/) or our [main page](https://biocomputeobject.org/)