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

John S. J. Anderson jacobs+usenet at genehack.org
Wed Aug 9 07:28:31 EST 2000

Hash: SHA1

jkb at arran.mrc-lmb.cam.ac.uk (James Bonfield) writes:

> 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 :-)

How much 'core' code versus 'interface'?

And I'm sure a few people would argue that well written code doesn't
happen by fluke... 8^)

> 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.

Interface is hard. Good interface is even harder, especially given
that the author(s) of bioinformatics software aren't going to be the
same type of user as Joe Pipetman. 

Command lines don't _have_ to be horrible, and can actually be quite
nice -- if you're the type of person who understand pipe lines, and
why they are a Good Thing. OTOH, authors who don't dump some
documentation in response to a 'foo -h' or 'foo --help' should be
smacked about the head and shoulders.


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