Acidbio
May 23, 2022 12:45 PM   Subscribe

Acidbio
Our new verification system, which tests for correct behavior in bioinformatics software packages. We crafted tests to unify correct behavior when tools encounter various edge cases—potentially unexpected inputs that exemplify the limits of the format. Inspired by the web standards Acid tests.
Role: principal investigator
posted by grouse (2 comments total)

Woot! Trying to put manners on binfo coders is a worthy aim. I cobbled up my first binfo software suite - to analyse synonymous codon usage for in-frame DNA sequence files - about 30 years ago. Even back then there were 10 different ways in which you could represent something as simple as the A T C Gs of sequence. We invented yet another format - a modified FASTA - because we believed it added utility to the output. But really it was just adding clutter to the collective. The fact that so few of your test cases were compliant does not surprise me one whit or jottle. I hope your project makes more waves than a single pub.
posted by BobTheScientist at 7:04 AM on May 28 [1 favorite]


Thanks BobTheScientist. There is increasing interest in standardization in genomics through Global Alliance for Genomics and Health standards body and much discussion of better testing and validation.
posted by grouse at 7:01 AM on May 30


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