BioCompute Conference and Workshop

From BCOeditor Wiki
Revision as of 16:45, 20 May 2024 by Kiran.sen (talk | contribs) (edit titles for speakers)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

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:

Please go to the FDA site for more transportation options.


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.


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 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)

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.

Conference Webinar

BioCompute Conference 2024 at FDA

Presented by the BioCompute team with plenary address by CBER Director Dr. Peter Marks

Published May 10, 2024

Watch Here

00:00 Intro - Jonathon Keeney, PhD

11:45 Vision and Future of Biocompute - Raja Mazumder, PhD, MS, MSC

28:48 FDA Alignment With The Vision of Biocompute - Peter W. Marks, MD, PhD

43:23 Biocompute Vision From an FDA-Industry Perspective - Vahan Simonyan, MD, PhD

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

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

1:21:23 Question Panel 1

1:42:14 Biocompute Objects and Workflows - Mark Walderhaug, PhD

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

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

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, PhD

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

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

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

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

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

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

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

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

05:36:32 Large Language Models - Konstantinos Krampis, PhD

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

06:07:28 BioCompute Library Project - Sean Keeney

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

06:16:16 BCOs to Unite Data and Workflow into Analysis - Patrick McNeely, MSc, PhD

06:19:20 Closing Remarks - Raja Mazumder, PhD, MS, MSc & Mark Walderhaug, PhD




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


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


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 Hadley King

Research Scientist, HIVE Lab, George Washington University

BioCompute Portal, BioCompute Database, and User Database: Why so many?
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.png
Peter Marks
Susan K. Gregurick.jpg
Susan K. Gregurick
Mazumder, Raja.jpeg.jpg
Raja Mazumder
Jonas Almeida.png
Jonas Almeida
Jun Luo.png
Jun Luo
Vahan Simonyan.png
Vahan Simonyan
Sam Westreich.jpg
Konstantinos Krampis.jpg
Konstantinos Krampis
Eric Donaldson
Dennis Dean.png
Dennis A. Dean, II
Virginia Hussong.jpg
Virginia Hussong
Keeney Jonathon 5309 MOD.jpg
Luis Santana-Quintero
Ben Sherman.png
Ben Sherman
Sean Kim.png
Sean Kim
Guangzhi Sun.jpg
Guangzhi Sun
Headshot for Hadley King
Hadley King
Stian Soiland-Reyes
Mark Walderhaug.jpg
Mark Walderhaug
Julia Maritz.jpg
Julia Maritz

Use Case Collection Form

Please take a moment to fill out our use case collection form here:

Contact Us

For questions about registration or general inquiries about BioCompute, please go to Contact Us or refer to our FAQs