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December 31, 2012 AT 12:58 am

Ten Simple Rules for the Open Development of Scientific Software

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PLOS Computational Biology: Ten Simple Rules for the Open Development of Scientific Software.

Open-source software development has had significant impact, not only on society, but also on scientific research. Papers describing software published as open source are amongst the most widely cited publications (e.g., BLAST, and Clustal-W), suggesting many scientific studies may not have been possible without some kind of open software to collect observations, analyze data, or present results. It is surprising, therefore, that so few papers are accompanied by open software, given the benefits that this may bring.

Publication of the source code you write not only can increase your impact, but also is essential if others are to be able to reproduce your results. Reproducibility is a tenet of computational science, and critical for pipelines employed in data-driven biological research. Publishing the source for the software you created as well as input data and results allows others to better understand your methodology, and why it produces, or fails to produce, expected results. Public release might not always be possible, perhaps due to intellectual property policies at your or your collaborators’ institutes; and it is important to make sure you know the regulations that apply to you. Open licensing models can be incredibly flexible and do not always prevent commercial software release.

Simply releasing the source under an open license, however, is not sufficient if you wish your code to remain useful beyond its publication. The sustainability of software after publication is probably the biggest problem faced by researchers who develop it, and it is here that participating in open development from the outset can make the biggest impact. Grant-based funding is often exhausted shortly after new software is released, and without support, in-house maintenance of the software and the systems it depends on becomes a struggle. As a consequence, the software will cease to work or become unavailable for download fairly quickly, which may contravene archival policies stipulated by your journal or funding body. A collaborative and open project allows you to spread the resource and maintenance load to minimize these risks, and significantly contributes to the sustainability of your software.

If you have the choice, embracing an open approach to development has tremendous benefits. It allows you to build on the work of other scientists, and enables others to build on your own efforts. To make the development of open scientific software more rewarding and the experience of using software more positive, the following ten rules are intended to serve as a guide for any computational scientist.

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