Ten Simple Rules for Taking Advantage of Git and GitHub

Published in PloS Computational Biology, 2016

Recommended citation: Perez-Riverol Y, Gatto L, Wang R, et al. Ten Simple Rules for Taking Advantage of Git and GitHub [published correction appears in PLoS Comput Biol. 2019 Jun 14;15(6):e1007142]. PLoS Comput Biol. 2016;12(7):e1004947. Published 2016 Jul 14. doi:10.1371/journal.pcbi.1004947 https://pubmed.ncbi.nlm.nih.gov/27415786/

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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 [1,2]. 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 [3,4]. 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 web-based 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.