[bip] Future of bioinformatics in python..?

[Peter Clarke]

Hello,

A little introduction, and then my 2 pence on the future of python in
bioinformatics..

I was introduced to Python by Titus in 2000 (thanks Titus, a lot!) and
having been using it ever since.

Currently we are hacking together different tools for comparative
sequence analysis of 70 yeast genomes. I am particularly interested in
network evolution and the mutational processes behind this. For this I
have been hacking bx-python and esperr (thanks James!) and pygr
(thanks Chris!).

We are also interested in non (protein) coding DNA and have been using
rpy and bioconductor for some tiling array analyses. Python and
RPy/Bioconductor are very useful for microarray analysis of all kinds.

We are also doing some dynamical systems models and I use SloppyCell
for this (http://sloppycell.sourceforge.net/)

I also use numpy, scipy, pytables, ipython, ipython1 for clusters,
pyrex, networkx, C++ boost graph library with python bindings,
MayaAvi, Ggobi. I use moinmoin and django for websites.

My 2 pence:

I think that the python bioinformatics community needs to come
together to form a project that can deliver something directly to the
end users (that caters for everyone from computationally naive
biologists to experienced programmers). This needs to be a systems
similar to Sage (http://www.sagemath.org/ - worth a look if you
haven't seen it before..) - possibly even building on top of it, to
tie many different tools together. This could be downloaded as a
package and would provide some sort of a user interface out the box
(as Sage and/or Galaxy - http://g2.trac.bx.psu.edu/) but then could
also easily be hacked. I think the Sage project is a good guide.

I would suggest, as  a start, incorporating everything mentioned above
in my intro along with anything else you all consider to be important.
I think this would only really work (and could work really well) if we
could make it a completely collaborative effort with everyone involved
in Python bioinformatics.

Any thoughts?

-Peter Clarke
http://www.mycib.ac.uk