{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T04:56:57Z","timestamp":1777438617030,"version":"3.51.4"},"reference-count":120,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2022,5,16]],"date-time":"2022-05-16T00:00:00Z","timestamp":1652659200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2015-03948"],"award-info":[{"award-number":["RGPIN-2015-03948"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Bioinformatics 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We 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\u2014potentially 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\u2019s performance on the test suite.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Acidbio is available at https:\/\/github.com\/hoffmangroup\/acidbio.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac327","type":"journal-article","created":{"date-parts":[[2022,5,16]],"date-time":"2022-05-16T07:48:02Z","timestamp":1652687282000},"page":"3327-3336","source":"Crossref","is-referenced-by-count":6,"title":["Assessing and assuring interoperability of a genomics file format"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5691-8238","authenticated-orcid":false,"given":"Yi Nian","family":"Niu","sequence":"first","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, ON, M5G 1L7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5398-358X","authenticated-orcid":false,"given":"Eric G","family":"Roberts","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, ON, M5G 1L7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8544-0026","authenticated-orcid":false,"given":"Danielle","family":"Denisko","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, ON, M5G 1L7, Canada"},{"name":"Department of Medical Biophysics, University of Toronto , Toronto, ON M5G 1L7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4517-1562","authenticated-orcid":false,"given":"Michael M","family":"Hoffman","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, ON, M5G 1L7, Canada"},{"name":"Department of Medical Biophysics, University of Toronto , Toronto, ON M5G 1L7, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"},{"name":"Vector Institute for Artificial Intelligence , Toronto, ON M5G 1M1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,16]]},"reference":[{"key":"2023041408001061300_","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1145\/1978542.1978557","article-title":"The robustness principle reconsidered","volume":"54","author":"Allman","year":"2011","journal-title":"Commun. 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