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Old 04-21-2011, 10:07 AM   #7
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

A great example of well documented and well written code can be found from the Broad (GATK, and especially Picard). How do we incentivize other groups or graduate students to produce quality and commented code beyond simple altruism? My advisor wanted it yesterday and there is a one-in-a-million case where the competing tool is better are opposite to this goal.

An extreme requirement would be that if any software is being produced as part of a grant, the code documentation system (javadoc/doxygen/etc) as well as the coding standards are proposed. We could also educate biologists (non-programmers) on the importance of good software engineering practices (beyond timeliness).
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