[bip] welcome!

[James Taylor]

My focus is mostly on vertebrate comparative genomics, I'm primarily  
interested in how regulatory information is encoded in genomes,  
(particularly vertebrates). Getting a handle on this leads to a  
variety of research directions, and I tend to use Python in  
everything I do since it is both fast to implement with and very  
powerful. I'm also interested in interface design and approaches for  
easily making powerful computational science tools available to  
experimental biologists. My public Python projects include:

   bx-python: some useful modules for large-scale genomics /  
comparative genomics (http://bx-python.trac.bx.psu.edu/)

   ESPERR and the Regulatory Potential score: methods for learning  
sequence / evolutionary signals from multiple genome alignments,  
chiefly focused on identification of vertebrate cis-regulatory  
modules. (http://www.bx.psu.edu/projects/esperr/)

   Galaxy: A web application for scientific analysis integrating a  
variety of tools and data-sources. (http://g2.trac.bx.psu.edu/)

I think this list is a great idea, and I'm interested in discussing  
how to share "infrastructure" in the biology-in-python community.  
Particularly, the merits of and problems with monolithic packages  
like biopython, and alternative models (e.g. how can we be more agile  
while still sharing common interfaces where sensible). But that is a  
discussion for another day...

-- jt

On Jul 25, 2007, at 12:01 PM, Titus Brown wrote:

> I'm curious -- what does everyone do, and what do they use Python for?