Organizing your computational biology projects
There’s a nice piece recently in PLoS Computational Biology on organizing your projects:
A quick guide to organizing computational biology projects
William S. Nobel
PLoS Computational Biology 2009
I can’t say I’m following all the advice here. I generally tend to leave a bit of a mess in my projects and every time I’ve completed one I’m vowing to do better next time, but here at least are some advice to keep in mind…
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August 31st, 2009 at 10:23 pm
Ugh. He actually suggests hardcoding file names in scripts. This always has struck me as amateurish, as running an existing script on new data would require editing the script. Personally, I’ve always tried to make my scripts to be as reusable as possible, with running the script without arguments giving a useful list of arguments and options, just like well written UNIX programs do.
September 1st, 2009 at 5:20 am
I actually do the hardcoding myself, whenever it isn’t an option I am going to change all the time. If the latter, I leave it as an option for the script but then prefer to have a Makefile with the script calls…