open-source software for bioinformatics (was Re: Unix vs Linux - the movie.)

Catherine Letondal letondal at nefertiti.pasteur.fr
Tue Aug 1 03:09:22 EST 2000


In article <87em4abii3.fsf at genehack.org>, "John S. J. Anderson" <jacobs+usenet at genehack.org> writes:
>>>>>> "Al" == alrichards  <alrichards at my-deja.com> writes:
>
>Al> How much bioinformatics research does not involve program code? 
>Al> Answer probably not much. Even paper which make use of standard
>Al> programs such as BLAST probably make use of some home grown
>Al> programs to sort/collate/ process the results.
>
>I honestly have no idea how many papers feature original code. I guess
>I'm not as concerned with code that just re-arranges the data set (the
>'sorting/collating' part of your comment), but code that 'processes'
>should probably be reviewed. On the plus side, it should be pretty
>simple code.
>
>Al> What fraction of the editorial boards of the major journals would
>Al> have the time or ability to take a program apart line-by-line? 
>Al> Answer - very few.
>
>I don't think the editorial boards should be doing this,
>necessarily. I think the anonymous peer reviewers _should_ be, by all
>means. 

One of the big benefit I could see for actual programs to be reviewed (well,
may be not line by line...) is that programming would be acknowledged as proper
scientific work. Which isn't the case at all currently (at least in France, I
don't know for other countries). And this sometimes prevent biologists to program.

-- 
Catherine Letondal -- Pasteur Institute Computing Center







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