Events

Welcome! This is the BioCompute Events page. Workshops are listed on the schedule below. For any questions, comments, or for a BioCompute Informational Session (15 minute WebEx) click here

Table of contents

• BioCompute Database and Transfer Mechanism Development Workshop
• BioCompute Objects on High-performance Integrated Virtual Environment (HIVE)
• Workflow Preservation and Reproducibility with BCO-RO
• Towards Interoperability: Generating BioCompute Objects on Cloud-Based Platforms for Advancing Precision Medicine
• Introduction to workflow portability with BCO-CWL
• BioCompute Advisory Boards Workshop
• BioCompute in the Microbiome: Building a Healthy Gut Database and Microbial Populations in Epilepsy
• BioCompute in the AVTIG Webinar series
• BioCompute in the MODSIM Webinar series
• BioCompute Workshop for Reviewers: Tool for Communicating Sequencing Analysis
• BioCompute at Biocuration 2020
• BioCompute at FDA SCB 2020
• BioCompute Objects: Tools for Communicating NGS Data and Analysis
• BioCompute Objects PoC Workshop
• 2014 Public Workshop: Next Generation Sequencing Standards

Previous Events

2022

BioCompute Database and Transfer Mechanism Development Workshop

Date: Wednesday January 12, 2022

Purpose: The purpose of this workshop is to demonstrate the tools available via the BioCompute Objects Portal, and how they enable interoperability in both research and regulatory review for scientists in the public or private spaces, and especially from the perspective of FDA personnel. As part of the larger goal of improving communication between the FDA and private sector and reducing organizational burden on both ends, this workshop will first introduce how the BioCompute Portal can build BioCompute Objects (BCOs) for workflow capture and reproducibility. The BioCompute Portal provides a framework for supporting workflow capture and improving reproducibility by providing user-friendly tools such as the BioCompute Object Builder (BCOB) that enables the creation of 2791-2020-compliant BCOs without requiring a user to know any code. We will demonstrate how the Portal can be securely used to manage, create, transfer, and publish objects that contain sensitive information. The BioCompute Portal presentation will also include the BioCompute Documentation site to introduce new users and acclimate current users to the newly restructured site. Following the introduction, we will walk through how a new user would sign up for an account on DB, the account activation process, and dashboard preview. This demo will also highlight the difference between a registered users’ dashboard and an unregistered public user’s, including access to user resources (best practices, user guide, etc.). Portal infrastructure could be extended to any company or institution that would like to establish their own private DB using the open-source repository and documentation on GitHub (https://github.com/biocompute-objects/bco_api). This workshop will demonstrate how the BCO framework is integrated into external platforms by showcasing the BCO transfer mechanism(s) from external resources to the Portal via API.

• Slides here
• Workshop recording here

2021

BioCompute Objects on High-performance Integrated Virtual Environment (HIVE)

Date: Saturday March 27 2021

• Slides here

Workflow Preservation and Reproducibility with BCO-RO

Date: Wednesday May 12 2021 at 11:00AM-12:30PM ET

Purpose: Training session showing how Research Objects (RO) can package BioCompute Objects (BCO) for Digital Preservation and Reproducibility. Research Objects (RO) are a machine-readable digital preservation effort that aims to package all constituent elements of an analysis together into one archive with very detailed provenance. Here, Stian Soiland-Reyes, a Technical Architect on the Research Objects project, will describe an example that packages the workflow as a descriptive, human-readable report in the form of a BioCompute Object (BCO), and which bundles everything in an RO “Crate.” Stian will explain the Research Objects project, and introduce a tutorial for building an RO-BCO archive. RO-BCOs can be efficient solutions for scaling up data analyses, both for internal record keeping and logistics, and for communicating workflows to outside groups.

• Slides here
• Workshop Recording here

Towards Interoperability: Generating BioCompute Objects on Cloud-Based Platforms for Advancing Precision Medicine

Date: Wednesday July 28 at 11:00AM-12:30PM ET

Purpose: The purpose of this workshop is to understand the value of interoperability in both research and regulatory review for scientists in the public or private spaces, and especially from the perspective of FDA personnel. As part of the larger goal of smoothing communication between the FDA and private sector to reduce organization burden on both ends, this workshop will first introduce how the cloud computing platform Seven Bridges can package BioCompute Objects (BCOs) for workflow capture and reproducibility. Following the introduction, we will describe several previously observed use cases to solicit feedback on their relevance to attendees, potentially from image processing (for diagnosis), machine-learning (for communicating and exchanging models with training data), and/or multi-modal data applications. Agenda can be found on the registration page.

Speaker: Dr. Dennis A. Dean, II is a Principal Investigator at Seven Bridges. He manages and builds interdisciplinary teams that develop complex tools and conduct data analyses from conception to deployment/completion. He leads the Translational Science and Analytics Team that includes data scientists, bioinformaticians, and genomic data scientists. He is responsible for the success of his team members across commercial, government, and internal projects. He leads collaborations with the U.S. Food and Drug Administration (FDA), the U.S. Department of Veteran Affairs Million Veteran Program (MVP) and collaborates with large pharmaceutical companies. Dr. Dean trained as a research fellow in medicine at the Harvard Medical School and Brigham and Women’s Hospital in the Program for Sleep Epidemiology and the Program for Sleep and Cardiovascular Medicine. He earned his Ph.D. in biomedical engineering and biotechnology and M.S. in computer science from the University of Massachusetts. He earned his B.S. in computer science from SUNY, Empire State College.

2020

BioCompute Advisory Boards Workshop

Date: Wednesday March 18, 2020 2-4pm ET

Purpose: The purpose of this workshop is to facilitate dialogue between Advisory Board(s) members on BioCompute applications, vocabulary, and current + future progression of the project through a hands-on approach. These discussions are a means to obtain feedback, introduce potential use-cases, and bring everyone up to speed about BioCompute.

• Slides here

BioCompute in the Microbiome: Building a Healthy Gut Database and Microbial Populations in Epilepsy

Date: Wednesday March 23, 2020

Slides here

BioCompute: A Standardized Method to Communicate Bioinformatic Workflow Information and Ease Organizational Burden

Part of the Advanced Virus Detection Technologies Interest Group Webinar series Date: Thursday April 2, 2020 Purpose: The purpose of this workshop is to []

• Slides here

MODSIM

Part of the MODSIM Interest Group Webinar series Date: Thursday April 21, 2020

• Slides here

BioCompute Workshop for Reviewers: Tool for Communicating Sequencing Analysis

Date: Wednesday June 24, 2020 10am-12pm ET

Purpose: The purpose of this workshop is to facilitate dialogue and show BCO utility specifically for FDA reviewers. We will be briefly discussing BioCompute applications, vocabulary, current + future progression of the project in addition to a hands-on approach to reviewing a BCO for. These discussions are a means to introduce BCO as a tool for submission evaluation mechanism obtain feedback.

• Slide deck available here

BioCompute Objects: Methods for communicating provenance of data and analysis

Part of the Biocuration 2020 Online Workshop series Date: Thursday September 24, 2020 9am PT, 12pm ET, 5pm CET

Purpose: Inform about BioCompute Object use and purpose and offer tutelage in the creation and use of BCOs

• Abstract available here
• Slides available here

BioCompute at FDA SCB 2020: Progress Towards the BioCompute Database

Date: Thursday November 5th 2020

• Slides available here

Introduction to workflow portability with BCO-CWL

Date': Friday November 20th 2020 at 12-2PM ET

Purpose: BioCompute Objects (BCOs) were developed to aid in communicating a more thorough understanding of computational analyses. While BCOs can be leveraged for re-execution within the context of specific platforms that have integrated them, they are not used for cross platform implementations. Common Workflow Language (CWL) was developed to assist in the portability of execution, meaning the ability to reproduce a pipeline in a different computational environment. The BCO and CWL teams have partnered over the last year to develop a joint mechanism that enables both portability of execution and strong human- and machine-readable documentation through metadata records. New functionality of BCO-CWL means that a reviewer may be able to independently run a computational pipeline used by a sponsor if using a command line environment, or on a platform that supports CWL. This presentation will go over the project by introducing the concept of portability of execution, the concept of a CWL file, and demonstrate the initial draft of a BCO-CWL implementation.