[Biopython-dev] ready for release?

Brad Chapman chapmanb at arches.uga.edu
Tue Dec 11 13:59:05 EST 2001

Hey Jeff;
Sweet. Glad we're getting this together. I just finished my last paper
early Monday morning and am rolling together some lab stuff I've been
working on right now, so I should have some time over the next week to
work on this. So it's a good time, I think :-)

> We've got a lot of new stuff, so I think it's time to roll a new
> release.  This will still be an alpha release, which means that new
> features are ok, as long as they're relatively bug-free.

Okay, I've got a bunch of code that could be checked in. Here's the

=> Generic Application Framework (Bio/Application). This is basically
what I wrote about previously; a general way to construct commandlines
for programs. This includes a commandline for BLAST
(Bio/Blast/Program.py) and functionality for running any commandline.
This Application stuff also interacts with BioCorba, so it is very cool;
I think :-)

=> Parsers and commandline interfaces for some Emboss primer-related
programs (primer3 and primersearch). Bio/Emboss/Primer.py and Program.py
plus some martel definitions.

=> Neural Network code (Bio/NeuralNetwork). Back propagation neural
networks, plus code to convert sequences as inputs into Neural networks.

=> Basic Hidden Markov Models (Bio/HMM). This includes Standard
and Baum Welch trainers and Viterbi prediction, all based heavily on
the Durbin et al book. 

=> Genetic Algorithm code (Bio/GA). This includes a fairly general
Genetic Algorithm framework, so isn't biology specific, but useful.

=> Drawing code that interacts with the reportlab pdf generation library
(Bio/Graphics). This makes it easier to draw pretty pictures of
chromosomes, and some other chart and graph stuff.

Whew, I think that's it. The code has all been used in real life
applications (which is why I wrote it :-), and has fairly good tests
written in the standard biopython style. The lacking thing is
documentation; I haven't been able to get myself up to writing docs for
a while (too many damn papers for classes, I guess :-).

What do people think? Do you want any of this? Which modules? Do you
want me to make a tarball of the code so you can look at it? If you just
want to glance, this is in CVS at:


Let me know what you guys think. I'm very happy to donate this to
biopython if you want it, and think I should have time over the next
week to check it all in and everything.

All-done-blathering-now-ly yr's

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