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

Kevin Karplus karplus at cse.ucsc.edu
Mon Aug 7 14:02:53 EST 2000

In article <8m8958$prc$1 at slb1.atl.mindspring.net>, "Andrew Dalke" <dalke at acm.org> writes:
|> So if you assume a 4,000 line program then the review takes about
|> 4 days, or around 24 hours, which is over twice the time you estimated
|> for a paper review.

The programs I have been writing lately for bioinformatics are more
like 13,000 lines, not counting the library we've developed (about
another 52,000 lines).  I suspect that many other bioinformatics
programs are that long or longer, and many are poorly written.  Asking
peer reviewers to read these programs (or sign non-disclosure
agreements) would result in no peer review ever happening.  I hesitate
now before taking on a 5-10-hour committment to review a paper---I would
certainly refuse a 60-100-hour comittment to read a program.

No one is going around checking that the lab protocols described in
papers are precisely executed---it is assumed that the experimenters
have normal competence.  Nor is it required that someone publishing a
sequence submit their sequencer hardware and software to peer review.
Why are people advocating an impossibly higher standard of peer review
for bioinformatics publications?

I susggest it is because some people do not want to pay for software
(though they seem to have no objection to paying enormous amounts for
reagents and lab equipment).  We routinely see requests on bionet
newsgroups for help in stealing software.

I applaud the programmers who provide open source and am glad to
encourge more open source.  But requiring that all scientific code
follow a particular philosophy is a sure way to stifle innovation.

Kevin Karplus 	karplus at cse.ucsc.edu	http://www.cse.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck
Anything below this line is junk added by others without my approval.

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