{"fb13147c5d49c991179550f33cb3ebdehermann":{"DOI":"10.1093/bib/bbw134","ISBN":"","ISSN":"1477-4054","URL":"https://doi.org/10.1093/bib/bbw134","abstract":"Investing in documenting your bioinformatics software well can increase its impact and save your time. To maximize the effectiveness of your documentation, we suggest following a few guidelines we propose here. We recommend providing multiple avenues for users to use your research software, including a navigable HTML interface with a quick start, useful help messages with detailed explanation and thorough examples for each feature of your software. By following these guidelines, you can assure that your hard work maximally benefits yourself and others.","annote":"","author":[{"family":"Karimzadeh","given":"Mehran"},{"family":"Hoffman","given":"Michael M"}],"citation-label":"karimzadeh2017considerations","collection-editor":[],"collection-title":"","container-author":[],"container-title":"Briefings in Bioinformatics","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2017","01"]],"literal":"2017"},"event-place":"","id":"fb13147c5d49c991179550f33cb3ebdehermann","interhash":"c7e73a48cc16904acd7afeb243f9bb1f","intrahash":"fb13147c5d49c991179550f33cb3ebde","issue":"4","issued":{"date-parts":[["2017","01"]],"literal":"2017"},"keyword":"forschungsdaten software recommendation diss","misc":{"eprint":"https://academic.oup.com/bib/article-pdf/19/4/693/25193101/bbw134.pdf","issn":"1477-4054","doi":"10.1093/bib/bbw134"},"note":"","number":"4","number-of-pages":"6","page":"693-699","page-first":"693","publisher":"","publisher-place":"","status":"","title":"Top considerations for creating bioinformatics software documentation","type":"article-journal","username":"hermann","version":"","volume":"19"},"c339bc95af1451e1bfa414d3e063f714hermann":{"DOI":"10.1186/2047-217X-3-31","ISBN":"","ISSN":"","URL":"","abstract":"Research in the context of data-driven science requires a backbone of\r\n   well-written software, but scientific researchers are typically not\r\n   trained at length in software engineering, the principles for creating\r\n   better software products. To address this gap, in particular for young\r\n   researchers new to programming, we give ten recommendations to ensure\r\n   the usability, sustainability and practicality of research software.","annote":"","author":[{"family":"Hastings","given":"Janna"},{"family":"Haug","given":"Kenneth"},{"family":"Steinbeck","given":"Christoph"}],"citation-label":"hastings2014recommendations","collection-editor":[],"collection-title":"","container-author":[],"container-title":"GIGASCIENCE","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2014","DEC 4"]],"literal":"2014"},"event-place":"236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND","id":"c339bc95af1451e1bfa414d3e063f714hermann","interhash":"f3537561d112ec6aa23e044f853131f4","intrahash":"c339bc95af1451e1bfa414d3e063f714","issue":"","issued":{"date-parts":[["2014","DEC 4"]],"literal":"2014"},"keyword":"forschungsdaten documentation software recommendation diss","misc":{"author-email":"{hastings@ebi.ac.uk}","language":"{English}","researcherid-numbers":"{Haug, Ove Kenneth/O-3809-2019\r\n   Haug, Kenneth/AAD-4241-2019\r\n   Haug, Ove Kenneth/D-8694-2017\r\n   }","oa":"{DOAJ Gold, Green Published}","affiliation":"{Hastings, J (Corresponding Author), European Bioinformat Inst, European Mol Biol Lab, Cheminformat \\& Metab, Wellcome Trust Genome Campus, Hinxton CB10 1SD, England.\r\n   Hastings, Janna; Haug, Kenneth; Steinbeck, Christoph, European Bioinformat Inst, European Mol Biol Lab, Cheminformat \\& Metab, Hinxton CB10 1SD, England.}","usage-count-last-180-days":"{0}","web-of-science-categories":"{Biology; Multidisciplinary Sciences}","article-number":"{31}","number-of-cited-references":"{12}","research-areas":"{Life Sciences \\& Biomedicine - Other Topics; Science \\& Technology -\r\n   Other Topics}","eissn":"{2047-217X}","times-cited":"{4}","orcid-numbers":"{Haug, Ove Kenneth/0000-0003-3168-4145\r\n   Hastings, Janna/0000-0002-3469-4923\r\n   Steinbeck, Christoph/0000-0001-6966-0814}","usage-count-since-2013":"{8}","doc-delivery-number":"{CX4HC}","da":"{2021-05-27}","journal-iso":"{GigaScience}","unique-id":"{ISI:000365658900002}","doi":"{10.1186/2047-217X-3-31}"},"note":"","number":"","page":"","page-first":"","publisher":"BIOMED CENTRAL LTD","publisher-place":"236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND","status":"","title":"Ten recommendations for software engineering in research","type":"article-journal","username":"hermann","version":"","volume":"3"},"b3444488cffac8a5783daba56155426ahermann":{"DOI":"10.1371/journal.pcbi.1005412","ISBN":"","ISSN":"","URL":"https://doi.org/10.1371/journal.pcbi.1005412","abstract":"Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer’s computer. We present ten simple rules to make such software robust enough to be run by anyone, anywhere, and thereby delight your users and collaborators.","annote":"","author":[{"family":"Taschuk","given":"Morgan"},{"family":"Wilson","given":"Greg"}],"citation-label":"taschuk2017simple","collection-editor":[],"collection-title":"","container-author":[],"container-title":"PLOS Computational Biology","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2017","04"]],"literal":"2017"},"event-place":"","id":"b3444488cffac8a5783daba56155426ahermann","interhash":"5a71f8c7107551d18a1a9903e96ddc4d","intrahash":"b3444488cffac8a5783daba56155426a","issue":"4","issued":{"date-parts":[["2017","04"]],"literal":"2017"},"keyword":"forschungsdaten documentation software recommendation diss","misc":{"doi":"10.1371/journal.pcbi.1005412"},"note":"","number":"4","number-of-pages":"9","page":"1-10","page-first":"1","publisher":"Public Library of Science","publisher-place":"","status":"","title":"Ten 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As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start. This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. These practices, which encompass data management, programming, collaborating with colleagues, organizing projects, tracking work, and writing manuscripts, are drawn from a wide variety of published sources from our daily lives and from our work with volunteer organizations that have delivered workshops to over 11,000 people since 2010.","annote":"","author":[{"family":"Wilson","given":"Greg"},{"family":"Bryan","given":"Jennifer"},{"family":"Cranston","given":"Karen"},{"family":"Kitzes","given":"Justin"},{"family":"Nederbragt","given":"Lex"},{"family":"Teal","given":"Tracy K."}],"citation-label":"wilson2017enough","collection-editor":[],"collection-title":"","container-author":[],"container-title":"PLOS Computational Biology","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2017","06"]],"literal":"2017"},"event-place":"","id":"52258c43ea1cd7975786fbbc2a61182ehermann","interhash":"89d06301d19fe097e96f032d7499f4e1","intrahash":"52258c43ea1cd7975786fbbc2a61182e","issue":"6","issued":{"date-parts":[["2017","06"]],"literal":"2017"},"keyword":"forschungsdaten software recommendation diss","misc":{"doi":"10.1371/journal.pcbi.1005510"},"note":"","number":"6","number-of-pages":"19","page":"1-20","page-first":"1","publisher":"Public Library of Science","publisher-place":"","status":"","title":"Good enough practices in scientific computing","type":"article-journal","username":"hermann","version":"","volume":"13"},"9237db0ac7c931684efce687458fe177hermann":{"DOI":"10.3934/math.2016.3.261","ISBN":"","ISSN":"","URL":"https://doi.org/10.3934%2Fmath.2016.3.261","abstract":"","annote":"","author":[{"family":"Fehr","given":"Jörg"},{"family":"and Jan Heiland","given":""},{"family":"Himpe","given":"Christian"},{"family":"Saak","given":"Jens"}],"citation-label":"fehr2016practices","collection-editor":[],"collection-title":"","container-author":[],"container-title":"AIMS Mathematics","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2016"]],"literal":"2016"},"event-place":"","id":"9237db0ac7c931684efce687458fe177hermann","interhash":"3807a59c103582e652c0f28162204851","intrahash":"9237db0ac7c931684efce687458fe177","issue":"3","issued":{"date-parts":[["2016"]],"literal":"2016"},"keyword":"forschungsdaten software recommendation diss","misc":{"doi":"10.3934/math.2016.3.261"},"note":"","number":"3","number-of-pages":"20","page":"261--281","page-first":"261","publisher":"American Institute of Mathematical Sciences (AIMS)","publisher-place":"","status":"","title":"Best practices for replicability, reproducibility and reusability of computer-based experiments exemplified by model reduction software","type":"article-journal","username":"hermann","version":"","volume":"1"}}