July 22nd, 2020
FDA announces support for BioCompute! The July 22nd, 2020 edition of the Federal Register announced that the FDA now supports BioCompute (officially known as IEEE 2791-2020), and that the standard will be added to the Data Standards Catalog.
June 24th, 2020
BioCompute training for FDA Reviewers and administrators took place today virtually. The workshop introduced the core concepts of BioCompute, terminology, and walked through usage examples in the context of regulatory submission filings, taken from sample use cases organized with FDA Reviewers. The training was constructed with input from advisory boards, and was focused on receiving a BCO as part of a regulatory filing, rather than technical details. What kinds of information is included in a BCO, where to find relevant information in certain scenarios, and ways to use additional optional fields to include or ask for more information were presented. Supplemental training material like the quick reference guide (PDF) was also provided.
May 14th, 2020
The IEEE Standard, now known as 2791-2020, has officially published. The standard can be purchased through the IEEE website, and the open source Schema referred to in the standard can be accessed here.
March 18th, 2020
Training for FDA personnel begins! The BioCompute team met with FDA reviewers and administrators to discuss the needs of FDA personnel and how best to implement BioCompute training. In a series of workshops, tutorials, demonstrations, and other training exercises, the BioCompute team will work with FDA Reviewers and administrators to understand BCOs and interpret information in BCO format, and will discuss the Extension Domains for acquiring extra information.
January 30th, 2020
The IEEE Standards Association (IEEE SA) has officially approved P2791 for publication. This marks formal acceptance as a standard, and clears the way for publishing. P2791 is one of the first standards to go through the IEEE Open Source Pilot Project, meaning the source for the entire project is open source (currently available here). Updates will be posted when the standard is officially published.
January 8th, 2020
The Review Committee (RevCom) for the Institute of Electrical and Electronics Engineers (IEEE) voted to recommend approving P2791, the proposed standard that embodies the BioCompute specification. The specification is an open source document (viewable here) that describes the propsed standard, and the vote to approve is major milestone in the project’s development. The next step is for the Standards Association (IEEE SA) to vote on the proposed standard based on this recommendation. In the event that it is approved, P2791 will become a formal, IEEE recognized standard!
October 18th, 2019
The BCO Challenge on PrecisionFDA has closed. Reviewers are currently evaluating both the beginner and advanced tracks, and will report their top performers on the PrecisionFDA website. Congratulations to all who participated, and thank you for helping to build the BioCompute project!
September 23rd, 2019
We’re excited to announce a new program to build a BioComputeDB for the FDA. The database will be a publicly accessible mechanism to facilitate better scientific communication of workflows with little additional communication, outside of the initial submission. As part of the program, we will gather input regarding needs and use cases from FDA personnel that will be used to build the database, and we will train FDA reviewers and researchers. Initial workshops will begin at the FDA in early 2020.
July 14th, 2019
BioCompute will be represented at the 52nd annual Association of Pathology Chairs Meeting in Boston, MA July 21 - 24. To learn how BioCompute can help support innovation in pathology, please email Jonathon Keeney at firstname.lastname@example.org to speak in person, or visit the table near registration, where information will be available. #APC19Boston
May 14th, 2019
The 2019 BioCompute Workshop was hosted at the FDA on May 14th, 2019. The workshop featured presentations from FDA reviewers, private sector bioinformatics companies and analysis platforms, a patient advocacy representative, and academic researchers, including discussions of integrating other standards like Common Workflow Language and FHIR Genomics. The 2019 Workshop also had an outstanding discussion panel that explored the current challenges in communicating NGS analysis pipelines, and how BioCompute might help address those challenges, and kicked off a BioCompute Challenge on the PrecisionFDA platform.
March 27th, 2019
We’re excited to announce that a proposal to expand BioCompute usage through the development of BCOs in a cloud computing environment for Galaxy has been accepted by the National Science Foundation! The proposal will create a library of BCOs describing bioinformatic workflows on Amazon Web Services through the open source platform Galaxy. The proposal is part of Internet2’s cooperative agreement with the National Science Foundation, called Exploring Clouds for Acceleration of Science Project.
March 7th, 2019
The 2019 BioCompute Workshop registration site is live! The United States Food and Drug Administration (FDA) has partnered with the George Washington University to host the 4th BioCompute Workshop. More details can be found on the FDA’s website.
February 28th, 2019
The IEEE draft specification of P2791 has passed the Mandatory Editorial Coordination (MEC) review and was approved by the EMB Standards Committee. This has moved the draft specification to the ballot phase, and ballot invitations have been sent out. If you would like to participate in the balloting phase, please contact the P2791 Secretary, Jonathon Keeney, at email@example.com. The first iteration of the specification is a descriptive standard that will underpin all future, computationally integrated specifications.
January 17th, 2019
The PLoS Bio paper describing the BioCompute project has been featured on the PLoS Open Source Toolkit! The Open Source Toolkit is a global forum for open source hadware and software. Its forum helps BioCompute reach a wider audience and cement its status as an invaluable specification for the communication of high throughput sequencing analysis. The paper is currently the first paper in “Featured Research.”
December 31st, 2018
Several members of the BioCompute community, in both the public and private sectors, have joined together to publish a manuscript describing the BioCompute project. The theory, utility, and implementation of the BioCompute specification are described, along with use cases.
December 23rd, 2018
The P2791 Working Group to build an IEEE BioCompute standard has formally voted to move ahead with the process. This means that the IEEE Sponsor will review the document, followed by an official Ballot Group review, and a public comment period. This is exciting news, and a major step for BioCompute. Standardization of BioCompute will create a formal mechanism for creating, commenting on, and using a way to communicate next generation sequencing data in a consensus-driven way.
October 1st, 2018
In order to explore the possibility of joining the Open Source Pilot Project, the BioCompute IEEE Working Group (P2791) meeting originally scheduled for October 5th has been postponed to October 22nd, 2018, at 1PM Eastern. The meeting will be held by WebEx at that time. This meeting is open to the public.
September 19th, 2018
2019 BioCompute Workshop announced! The next BioCompute Workshop will be held on March 25th, 2019 at the FDA’s White Oak campus. A Scientific Advisory Board will be formed and convened to discuss the agenda and speakers.
September 11th, 2018
BioCompute is presented at the IEEE Standards Association Workshop: Standards for Digital Data in Ehealth. The workshop, hosted by the IEEE Standards Association, explored standards in cutting edge technologies being deployed in healthcare. As a mechanism to bridge efforts between researchers, clinicians, and the regulatory pipeline, BioCompute helps to advance personalized medicine by enabling better communication between these key drivers.
August 29th, 2018
Kickoff meeting for the IEEE Working Group convened! The IEEE Working Group, P2791, has held its first meeting. The meeting was well attended by representatives from the FDA, as well as several universities, biotech, and pharmaceutical enterprises. With a core constituency of voting members established, future Working Group meetings will work to establish Version 1.3 of the Specification Document into a formal IEEE Standard.
July 24th, 2018
As part of its efforts to host NIH funded data sets through the STRIDES program, Google today announced that it will use the BioCompute standard to help make these datasets more accessible. BioCompute helps build transparency and reproducibility into work flows in the high throughput sequencing space, and will improve the utility of NIH funded datasets.