BioCompute Conference and Workshop
2024 BioCompute Conference and Workshop
This workshop provides an opportunity to learn aboutan 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 AI/ML- related BCO implementations. We encourage everyone to attend in person for hands-on experience, discussion and poster session.
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:
- College Park Metro (Green line)
- Glenmont Metro (Red line)
- Medical Center Metro (Red line)
- Shady Grove Metro (Red line)
- Silver Spring Metro (Red line)
- Twinbrook Metro (Red line)
- More FDA shuttle info can be found here
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
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)
Workshop Topics
- Updates and future for BioCompute
- Need for BCO at FDA
- Considerations for Adoption in Industry
- Progress Towards Usability
- 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
Poster Session
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.
Content: Any chosen workflow that can engage BCO. More detail coming.
Size: poster sizes can be up to 4' tall x 6' wide.
Submission: Submission portal coming soon.
Schedule
| Time | Speaker | Content/Title |
|---|---|---|
| 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
| Sam Westreich - DNAnexus | Konstantinos Krampis | Elaine E. Thompson, Ph.D. |
Dennis A. Dean, II - Velsera
Phil Webster- Velsera
Jonathon Keeney - The George Washington University (GWU)
Charles Hadley King - The George Washington University (GWU)
Omar Serang - DNAnexus
Contact Us
For questions about registration or general inquiries, please go to Contact Us