BioCompute Conference and Workshop: Difference between revisions
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== <big>Use Case Collection Form</big>== | == <big>Use Case Collection Form</big>== | ||
<big>Please take a moment to fill out our use case collection form here: | <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>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> | <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> |
Revision as of 20:51, 7 May 2024
2024 BioCompute Conference and Workshop
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.
Event Registration: Eventbrite
Date & Time: May 10th, 2024, 9 AM - 5 PM
Location: Great Room, White Oak Campus, FDA center
Getting there
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.
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.
Accommodation
If you require accommodation during your stay, please refer to the following document for a list of hotels near the FDA White Oak Campus: Hotels by the FDA White Oak Campus. This resource provides information on nearby accommodations to ensure your comfort and convenience during the event.
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
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.
Abstract: Any computational workflow of interest, or topic related to BCOs
Poster Content: Posters should highlight or describe a workflow (either in progress or one already in use) and the way it is used.
Size: poster sizes can be up to 4' tall x 6' wide.
Submission Portal: click here.
Schedule
Morning
Session |
Time | Speaker | Content |
---|---|---|---|
9:00 - 10:00AM | Introduction and Future for BioCompute | ||
9:00 - 9:15 | Jonathon Keeney
Research Assistant Professor, George Washington University |
Welcome and Introduction | |
9:15 - 9:30 | Raja Mazumder
Professor, George Washington University |
Vision and Future of BioCompute | |
9:30 - 9:45 | Peter Marks
Director, CBER, FDA |
Plenary Address | |
9:45 - 10:00AM | Break | ||
10:00 - 10:55AM | Considerations for Adoption in Industry | ||
10:00 - 10:15 | Vahan Simonyan
CSO, Embleema, DNA HIVE |
BioCompute Vision from an FDA-Industry Perspective | |
10:15 - 10:30 | Jun Luo
Data Scientist, Novo Nordisk |
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
Senior Scientist, Merck |
Applications of BioCompute Objects for Viral Metagenomics Analysis | |
10:45 - 10:55 | Discussion | ||
10:55 - 11:10AM | Break and poster review | ||
11:10 - 12:05PM | Need for BCO at FDA | ||
11:10 - 11:25 | Mark Walderhaug
Associate Director for Risk Assessment, CBER, FDA |
BioCompute Objects and Workflows | |
11:25 - 11:40 | Luis Santana-Quintero
HIVE lead, CBER, FDA |
Computational Reviews at CBER | |
11:40 - 11:55 | Eric Donaldson
Clinical Virology Reviewer |
Perspectives from a Reviewer: High Throughput Sequencing Data Challenges in FDA Regulatory Review | |
11:55 - 12:05 | Discussion | ||
12:05 - 1:10PM | Lunch & Poster Session | ||
Afternoon
Session |
1:10 - 4:30PM | Technical, Administrative, and Usability Session | |
1:10 - 1:25 | Susan Gregurick
Director of Data Science, NIH |
AI for Health and Research: Exploring NIH’s Strategies, Challenges, and Vision for the Future | |
1:25 - 1:40 | Virginia Hussong
Miscellaneous Administration and Program, FDA |
Forthcoming Guidance for BCO Submission | |
1:40 - 1:55 | Guangzhi Sun
Associate Researcher, China National Institute of Standardization (CNIS), ISO |
Extending BCO specification into a Generic Metamodel for Computable Data | |
1:55 - 2:10PM | Break and Poster review | ||
2:10 - 2:25 | Jonas Almeida
Director of Data Science, Division of Cancer Epidemiology and Genetics, NCI |
Functionalization of Biocompute Objects using Generative AI | |
2:25 - 2:40 | Sam Westreich
Sr. Scientific Program Manager, DNAnexus |
DNAnexus: Democratizing access to BCOs with the BCOnexus Platform-Free Editor | |
2:40 - 3:00 | Dennis Dean
Director of Translational Sciences, Velsera |
Facilitating BCO Use from Standard to Best Practices: The Neoantigen Workflow Use Case | |
3:00 - 3:15 | Steph Singleton
Bioinformatics Scientist, Technical Project Manager, Essential Software Inc. |
Capturing Machine Learning Pipelines via BioCompute Objects | |
3:15 - 3:30PM | Break and Poster review | ||
3:30 - 3:45 | Stian Soiland-Reyes and Meznah Aloqalaa
Senior Lecturer, University of Manchester/Ph.D. Student |
BCO, Provenance Models (PRIMAD, RO-Crate) and FAIR Computational Workflows | |
3:45 - 4:00 | Ben Sherman
Developer, Seqera Labs |
Generating BioCompute Objects for Nextflow Pipelines | |
4:00 - 4:15 | Konstantinos Krampis
Associate Professor of Biology and Computer Science, CUNY |
BCO in AI: Leveraging Large Language Models (aka ChatGPT) for Biocompute Object Generation in Bioinformatics | |
4:15 - 4:30 | Sean Kim
Bioinformatics Specialist, George Washington University |
Enhanced BioCompute Object Creation through Retrieval-Augmented Generation from Scientific Papers | |
4:30 - 4:40PM | Break and Poster review | ||
4:40 - 5:00PM | Lightning talk and closing | ||
4:40 - 4:55 | Chosen speakers | Poster lightning talks | |
4:55 - 5:00PM | Closing
Mark Walderhaug and Raja Mazumder |
Confirmed Presenters
Peter Marks
|
Susan K. Gregurick
|
Raja Mazumder
|
Jonas Almeida
|
Jun Luo
|
Vahan Simonyan
|
Konstantinos Krampis
|
Eric Donaldson
|
Dennis A. Dean, II
| |
Virginia Hussong
|
Luis Santana-Quintero
|
Ben Sherman
|
Sean Kim
| |
Guangzhi Sun
|
Stephanie Singleton
|
Stian Soiland-Reyes
|
Mark Walderhaug
|
Julia Maritz
|
Use Case Collection Form
Please take a moment to fill out our use case collection form here: https://docs.google.com/forms/d/e/1FAIpQLSfS5E-cpPMvIdEHVqPiZnmcpsH5JetMsBAY2vnsemRWeDj5uw/viewform
Contact Us
For questions about registration or general inquiries about BioCompute, please go to Contact Us or refer to our FAQs