BioCompute Spring Workshop 2024: Difference between revisions

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{{DISPLAYTITLE:BioCompute Spring Workshop Summer 2023}}
#REDIRECT [[BioCompute Conference and Workshop]]
'''2024 BioCompute Conference and Workshop'''


''' This hybrid workshop provides an opportunity to learn about BioCompute Objects and interoperability between 3 platforms that host BioCompute Objects. It will also cover BCODB and Portal at the FDA, real-world applications, and potential AL/ML-related BCO implementations''
''<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 and discussion.</big>''  


'''Date & Time:''' May 10th, 2024, 8 AM - 5 PM
<big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big>


'''Location:''' Great Room, White Oak Campus, FDA center
<big>'''Date & Time:''' May 10th, 2024, 9 AM - 5 PM</big>


'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]
<big>'''Location:''' Great Room, White Oak Campus, FDA center</big>


== Abstract ==
==== <big>'''<u>Getting there</u>'''</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 describing workflows in a precise yet adaptable manner. 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>By Car</big>'''


As the field continues to evolve, 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>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>


The [https://www.biocomputeobject.org/ BioCompute Portal], serving as 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. Overall, this project strives to streamline and secure the submission process. 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.
<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]


== Workshop Topics ==
<big>Please go to the [https://www.fda.gov/about-fda/visitor-information/getting-fda FDA site] for more transportation options.</big>
* Updates on BioComput
* BCO Portal at the FDA
* Platform interoperability,
* Exemplar workflows and real-world applications
* BCO-Nextflow
* AI/ML-related implementations


== Schedule ==
== <big>Abstract</big> ==
TBD
<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>


== Organization Committee ==
<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>
Mark Walderhaug - U.S Food & Drug (FDA)


Luis Santana-Quintero - U.S Food & Drug (FDA)
=== <big><u>Organization Committee</u></big> ===
TBD


Raja Mazumder - The George Washington University (GWU)
== <big>Workshop Topics</big> ==
* <big>Updates on BioCompute</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>


Jonathon Keeney - The George Washington University (GWU)
== <big>Schedule</big> ==
{| class="wikitable"
|+
!Time
!Speaker
!Content
|-
!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
|}


Charles Hadley King - The George Washington University (GWU)
== <big>Confirmed Presenters</big> ==
{| class="wikitable"
|+
!
!
!
!
|}
<big>[https://www.linkedin.com/in/jonathon-keeney/ Jonathon Keeney] - The George Washington University (GWU)</big>


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


Chinweoke Okonkwo - The George Washington University (GWU)
<big>[https://www.linkedin.com/in/omarserang/ Omar Serang] - DNAnexus</big>


Omar Serang - DNAnexus
<big>[https://www.linkedin.com/in/sam-westreich/ Sam Westreich] - DNAnexus</big>


Sam Westreich - DNAnexus
<big>Dennis A. Dean, II - Velsera</big>


Dennis A. Dean, II - Velsera
<big>[https://www.linkedin.com/in/phillipjwebster/ Phil Webster]- Velsera</big>


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

Latest revision as of 18:21, 6 February 2024

Redirect to:

2024 BioCompute Conference and Workshop

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 and discussion.

Event Registration: Eventbrite

Date & Time: May 10th, 2024, 9 AM - 5 PM

Location: Great Room, White Oak Campus, FDA center

Getting there

By Car

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 FDA website for the campus map.

By metro Public buses:

  • Ride On Bus Route 22 - stops at the Silver Spring (Red line) Metro station
  • BRT Flash Orange Route - stops at the Silver Spring (Red line) Metro station
  • Metro Bus C8 - stops at the White Flint (Red line), Glenmont (Red Line), and College Park (Green line) Metro stations
  • Metro Bus K6 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station
  • Metro Bus K9 - stops at the Fort Totten (Red, Green, and Yellow lines) Metro station

FDA shuttle to metro:

Please go to the FDA site for more transportation options.

Abstract

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.

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.

The 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.

Organization Committee

TBD

Workshop Topics

  • Updates on BioCompute
  • BCODB and Portal's use at the FDA
  • BCO platform interoperability
  • Exemplar workflows and real-world applications
  • BCO-Nextflow
  • Potential AI/ML-related implementations
  • FAQ session & Roundtable discussion

Schedule

Time Speaker Content
9:00 - 10:05 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 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 Discussion
11:00 - 11:20 Break and poster review
11:20 - 12:15 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 Lunch & Poster Session
1:15 - 4:10 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 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 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 Break and Poster review
4:05 - 5:00 Lightning talk and closing
4:05 - 4:45 Chosen speakers Poster lightning talks
4:45 - 5:00 Closing

Confirmed Presenters

Jonathon Keeney - The George Washington University (GWU)

Charles Hadley King - The George Washington University (GWU)

Omar Serang - DNAnexus

Sam Westreich - DNAnexus

Dennis A. Dean, II - Velsera

Phil Webster- Velsera

Contact Us

For questions about registration or general inquiries, please go to Contact Us

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