[bip] Reproducible research

[C. Titus Brown]

On Wed, Mar 04, 2009 at 06:56:12PM +0100, Giovanni Marco Dall'Olio wrote:
-> On Wed, Mar 4, 2009 at 4:16 PM, Andrew Dalke <dalke at dalkescientific.com> wrote:
-> > On Mar 4, 2009, at 12:14 PM, Giovanni Marco Dall'Olio wrote:
-> >> Another solution to reproducibility, in a perfect world, would be that
-> >> people write good tests for their programs.
-> >> Let's say that I write a program that predicts the coding sequences in
-> >> a nucleotide sequence.
-> >> If I provide good tests for it, people should be able to reproduce my
-> >> analisis and understand it even if they don't know the programming
-> >> language that I have used, or even without having to have the source
-> >> code of my scripts.
-> >
-> 
-> eheh, nice discussion :)
-> 
-> I understand that it is impossible to write full suites of tests for
-> an analysis or an experiment; but I was critizing the fact that nobody
-> seems to care about this problem.
-> If you look at the programs of any master or course in bioinformatics,
-> you'll see that none ever explain what an unit test is, or give
-> general ideas about the concept of testing.
-> Also, it is very difficult to find articles or discussion over this
-> topic, even online.

<rant>
That's because nobody cares if your code is right, just that you can
publish a good paper on the results from running it.  Once.
</rant>

Unfortunately doing both good code + good publication is an awful lot of
hard work, so if it's not rewarded *shrug*.

--titus