New Publication from the Hoffman Lab
The lab of MBP researcher Dr. Michael Hoffman recently published a new Bioinformatics article entitled ‘Assessing and assuring interoperability of a genomics file format’.
The manuscript explores, and proposes solutions to, the problem of interoperability in bioinformatics file formats with a focus on the Browser Extensible Data (BED) genomics file format. Through this work, Dr. Hoffman and his team, which included MBP MSc student Danielle Denisko, established a formal specification for BED through the Global Alliance for Genomics and Health (GA4GH) standards process. This led to the development of a new verification system called ‘Acidbio’, which tests for correct behaviour in bioinformatics software packages, and the creation of a test suite for BED.
The Hoffman lab has made the Acidbio system available publicly to make it easier for developers and others to test the conformance of new packages to the standard. Just as the Acid tests for web browsers ushered in a new era of widespread standards compliance, they hope that this approach will improve interoperability, and make bioinformatics analyses more robust.