ArticleBioinformatics (Oxford, England)2022
Assessing and assuring interoperability of a genomics file format.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Model Context Protocol: The unexpected catalyst of a bioinformatics interoperability revolution.PLoS computational biology · 2026Article
- CRISPR-BEasy: a free web-based service for designing sgRNA tiling libraries for CRISPR-dependent base editing screens.Nucleic acids research · 2025Article
- Regional-specific calibration enables application of computational evidence for clinical classification of 5' cis-regulatory variants in Mendelian disease.American journal of human genetics · 2024Article
- FAIR Header Reference genome: a TRUSTworthy standard.Briefings in bioinformatics · 2024Article
- Ten simple rules for developing visualization tools in genomics.PLoS computational biology · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationBioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, making it difficult or impossible for the creators of these tools to robustly test them for correct handling of input and output. This causes problems in interoperability between different tools that, at best, wastes time and frustrates users. At worst, interoperability issues could lead to undetected errors in scientific results.
resultsWe developed a new verification system, Acidbio, 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. To analyze the performance of existing software, we tested the input validation of 80 Bioconda packages that parsed the Browser Extensible Data (BED) format. We also used a fuzzing approach to automatically perform additional testing. Of 80 software packages examined, 75 achieved less than 70% correctness on our test suite. We categorized multiple root causes for the poor performance of different types of software. Fuzzing detected other errors that the manually designed test suite could not. We also created a badge system that developers can use to indicate more precisely which BED variants their software accepts and to advertise the software's performance on the test suite. AVAILABILITY AND IMPLEMENTATION: Acidbio is available at https://github.com/hoffmangroup/acidbio. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.