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I've written an analytical pipeline in Python that I think will be useful to other people. I'm wondering whether it is customary to publish such scripts in GitHub, whether there's a specific place to do this for Python scripts, or even if there's a more specific place for biology-related Python scripts.

David Cain
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Atticus29
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4 Answers4

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While there are many approaches to this, one of the customary solutions would be to indeed publish it on github and then link to it from your research institution's website.

0x90
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    see also : "On the Preservation of Published Bioinformatics Code on Github " http://caseybergman.wordpress.com/2012/11/08/on-the-preservation-of-published-bioinformatics-code-on-github/ – Pierre Nov 13 '12 at 07:20
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You could also publish it on sourceforge. All types of science, engineering, etc scripts are posted, and millions of people download these scripts. Github is also a good choice, but I do believe sourceforge is more popular in viewers and in downloads. Also, you could publish a openwetware wiki and post the code there, openwetware is a wiki system for scientific use, I have used it previously and recommend it. Or you can link the two great opensource platforms, sourceforge and github by mirroring so your project is essentially'synced' to both platforms: Check this out:

http://www.17od.com/2010/11/11/migrating-a-sourceforge-subversion-repository-to-github/ -overview http://www.xcore.com/forum/viewtopic.php?f=3&t=162 - how to actually mirror

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Another option would be to publish it on bioinformatics.org.

David L.
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see also "On the Preservation of Published Bioinformatics Code on Github"

Pierre
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