BioCompute Objects: Tools for Communicating Next Generation Sequencing Data and Analysis

Agenda for The 2019 BioCompute Workshop, co-sponsored by the U.S. Food and Drug Administration (FDA), the George Washington University, and the BioCompute Partnership

Date: Tuesday, May 14th, 2019, 9AM-5PM

Location: FDA White Oak Campus, 10903 New Hampshire Ave., Bldg. 31 Conference Center, room 1503 A, Silver Spring, MD 20993

Register: Eventbrite


Opening Remarks

9:00 - 9:10 AM

FDA Perspective

Carolyn Wilson


Perspectives to Inform BioCompute

9:10 - 9:35 AM

Layperson's Explanation of BCO Specification and Utility | IEEE and ISO Status

Raja Mazumder and Jonathon Keeney

An introduction to the BioCompute project for non-engineers, and a description of the standardization efforts and current status.
9:35 - 9:50 AM

The Importance of Standardized Workflows in Patient Advocacy

Jeanne Barnett
9:50 - 10:45 AM

Panel Discussion featuring Genomic Working Group and other stakeholders

Eric Donaldson (co-moderator), Heike Schitig (co-moderator), Dennis Dean, Gil Alterovitz, Jeanne Barnett, Jonas Almeida, Elaine Thompson, Arifa Khan, Errol Strain

- Define FDA NGS Research and Regulatory Need Generation

- Introduce Strategies for working with large amounts of data

- Discuss the challenges associated with communicating NGS workflows in clinical settings, security, implementation etc.

10:45 - 11:00 AM

Coffee Break



Operationalizing BCO Part I

11:00 - 11:10 AM

BCO Creation and Viewing in the HIVE Platform

Elaine Thompson & Mark Walderhaug
11:10 - 11:20 AM

The BioCompute Object Editor (bco_editor) Tool

Janisha Patel
11:20 - 11:30 AM

Seven Bridges Genomics BCO Creation

Dennis Dean
11:30 - 11:40 AM

From Bio-Docklets to Galaxy and back: BioCompute Objects for Standardized, Scalable Bioinformatics

Ntino Krampis
11:40 - 11:50 AM

Implementing Biocompute Objects to Address Bioinformatic Standardization for Whole Genome Sequencing of Mycobacterium Tuberculosis

Marco Schito
11:50 - 12:00 PM

Verification Kit Use Case: Technical Description

Anjan Purkayastha
12:00 - 12:10 PM

High Throughput Sequencing Communication with the FDA Through Trial Use of BCO with a Verification Kit

Eric Donaldson & Nuria Guimera
12:10 - 1:30 PM

Lunch Break



Operationalizing BCO Part II

1:30 - 1:50 PM

Multifaceted use of BCOs (Healthcare, physics, image analysis etc. and importance in IEEE and ISO process for broad usability)

Vahan Simonyan
1:50 - 2:00 PM

Re-executable BCOs with CWL & ResearchObjects

Michael Crusoe
2:00 - 2:10 PM

BCO Applications in Medicine with FHIR

Gil Alterovitz & James Jones
2:10 - 2:20 PM

BCO as a Manifest for Orchestrating Web API Ecosystems

Jonas Almeida
2:20 - 2:30 PM

Using BCOs to organize healthcare marketplace | Patient-driven Clinical Data Exchange

Robert Chu
2:30 - 3:00 PM

BCO Challenge on PrecisionFDA Platform Announcement

Overview of Precision FDA - Zivana Tezak
Discussion of future opportunities to integrate BCO into the precisionFDA platform - John Didion
App-a-thon announcement and details - Holly Stephens
Q&A
3:00 - 3:15 PM

Coffee Break



Next Steps, Q&A, and Training

3:15 - 3:25 PM

Summary and Next Steps

Raja Mazumder

Associate Professor of Biochemistry and Molecular Medicine, George Washington University, Co-Director of The McCormick Genomic and Proteomic Center

3:25 - 3:45 PM

Closing Remarks

Mark Walderhaug

Associate Office Director for Risk Assessment at U.S. Food & Drug Administration

3:45 - 5:00 PM

Q&A, BCO Training, and Hands-on Demos by the following teams:

HIVE (Naila Gulzar), Galaxy (Ntino Krampis and Nicola Soranzo), DNAnexus (John Didion), BCO Spec. use (Hadley King), BCO extensions and schema (Jason Travis)



*Coffee and lunch available for purchase at the onsite kiosk.