Version control for scientific research - BioMed Central blog

"We live in an increasingly collaborative era, where the Internet enables distance collaboration almost trivially – not just with e-mail and videoconferencing, but with collaborative realtime document editing and networked transmission of data and analyses. These tools allow us to collectively leverage many resources to rapidly solve problems and ultimately accelerate scientific discovery. While these tools and technologies are fundamentally changing how we collaborate on science, there is still considerable room for improvement in how we are using them. Programmers, and especially the world of open source software development, have developed a number of tools that enable easy distance collaboration and sharing of data and code. One of the most important is version control – tracking of changes and authorship – which, in programming, is largely used for writing and sharing code, tracking and annotating contributions, and resolving changes to the same section of a program. In recent years a wide variety of version control software has become readily and freely available, including Subversion, git, and Mercurial. Motivated by much the same problems as programmers – how do I track changes and authorship, and resolve conflicting changes? – scientists have increasingly begun using these version control systems not only for software but for paper and grant writing, and even for tracking data and metadata. In particular, CTB and others have argued that version control should be a required 'good practice' for all computational science in practice. This increased interest in versioning for science has led to a realization that, collectively, we are lacking in workflows and practices that take advantage of version control. This is especially true for git and Mercurial, both decentralized version control systems that enable many different modes of collaboration. One of us, KR, has just published a paper showing how 'git can facilitate greater reproducibility and increased transparency in science.' Occasioned in part by this first paper, a group of us is working to document and demonstrate the many uses to which we have put git. These include software development and dissemination, paper and grant writing, paper and grant feedback, contributions to Wiki-like community documentation sites, and sharing of data analysis 'notebooks' and executable papers. In tandem with git and Mercurial, two commercial Web sites have appeared, GitHub and BitBucket. These sites serve as central 'hubs' through which code and other electronic artifacts can be communicated, shared, and collaborated upon ..."