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

James Bonfield jkb at arran.mrc-lmb.cam.ac.uk
Tue Aug 8 08:17:11 EST 2000

In <398ef9cd$1 at news.ucsc.edu> karplus at cse.ucsc.edu (Kevin Karplus) writes:

> 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.

Indeed. Our assembly editor, gap4, is more like 200,000 lines (including a few 
of our own libraries). Undoubtably parts of poorly written too; and I contend
that some parts are well written - perhaps by fluke :-)

Perhaps more important than just "what's the code look like" is "what's the
documentation like?". MANY of the bioinformatics tools have truely hideous
command line interfaces which most users are going to run away from.

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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