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Public Library of Science, PLoS Computational Biology, 7(12), p. e1004947

DOI: 10.1371/journal.pcbi.1004947

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Ten Simple Rules for Taking Advantage of git and GitHub

This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Bioinformatics is a broad discipline in which one common denominator is the need to produce and/or use software that can be applied to biological data in different contexts. To enable and ensure the replicability and traceability of scientific claims, it is essential that the scientific publication, the corresponding datasets, and the data analysis are made publicly available. All software used for the analysis should be either carefully documented (e.g., for commercial software) or, better yet, openly shared and directly accessible to others. The rise of openly available software and source code alongside concomitant collaborative development is facilitated by the existence of several code repository services such as SourceForge, Bitbucket, GitLab, and GitHub, among others. These resources are also essential for collaborative software projects because they enable the organization and sharing of programming tasks between different remote contributors. Here, we introduce the main features of GitHub, a popular webbased platform that offers a free and integrated environment for hosting the source code, documentation, and project-related web content for open-source projects. GitHub also offers paid plans for private repositories (see Box 1) for individuals and businesses as well as free plans including private repositories for research and educational use. ; Wellcome Trust (London, England) (Grant WT101477MA) ; Biotechnology and Biological Sciences Research Council (Great Britain) (Grants BB/K01997X/1, BB/I00095X/1, BB/L024225/1 and BB/L002817/1) ; Germany. Federal Ministry of Education and Research (Grant FKZ031 A 534A) ; National Institutes of Health (U.S.) (Grants R01-GM-094231 and R01-EB-017205 ) ; Engineering and Physical Sciences Research Council (Grant EP/M022641/1) ; National Science Foundation (U.S.) (Grant 1252893) ; Novo Nordisk Foundation