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Old 04-22-2011, 02:23 PM   #13
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

To summarize, unit tests and code documentation are great make robust code and better communicate across developers. User documentation and usability allow the software to be used more easily by a wider group of people, making your software invaluable and more likely to receive software support funding. Most of this is software engineering 101.

Nonetheless, these are all indirect incentives, and are not built pro-actively into the funding or even training mechanisms; we have not talked about training individuals for software engineering (is this the PIs role and/or coursework?).

What I really want to see come from this discussion is how can we train and support computer scientists, bioinformaticians, and biologists so that they write well documented (user and code) usable software?

I will throw a suggestion of the top of my head to get the ball rolling. How about an open source software repository, like an bio-app store, which allows for a central repository of cutting edge (not ten release ago) bio-apps that have software that meet (or are ranked on) certain criteria on documentation, code standards, and portability. I am sure a grant reviewer would then find it easy to look up past software and say, person Y always produces well-documented and well-used software. Similarly, a requirement of applying for a grant that includes software is submission and release of software that meets these standards. Accountability and training is the key.
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