[BioPython] BOF at BOSC redux

[Jeffrey Chang]

Hello Everybody,

It was nice to meet you all at BOSC.  I'm pleased with the interest open
source software in biology, and especially with the interest in biopython.  
We had a very productive Birds-of-a-Feather session on biopython and
received valuable input from current users and potential users of the
libraries.

I am sending out a copy of the notes Andrew took, for the people who were
not able to make it.  Some of the issues we discussed were valuable, and I
hope that it guides our thinking for the future of the project.

Jeff




The agenda (which we didn't follow closely) was:
Introduction
  - comments
  - complaints
  - experiences
Tasks
  - how to help
  - Sequence class?
  - documentation
  - web site
  - biocorba
Wish List


Examples of why a biologist would use bipoython (applications)
  - restriction enzymes
  - revcomp, translate
  - give mRNA
  - mutate/modify/join, handle circular dna
  - SNP's
  - apply algorithms from computational chemistry to biology
  - support iterative development w/GUI's, DB's
  - work with pre-finished sequences (shotgun output)
  - should handle % certainty associated with base, quality scores
  - store drug/ligand interaction data
Structure stuff
  - small and big molecule structure data (MMTK?)
  - interface to structure prediction programs
  - structure object should interface to saequence
  - analysis of structure, H-bonds, ramachandran, phi/psi computation
distributed computing
  - mpi, dvm, soap, corba, etc
design philosophy
  - 1 standard class vs support to make your own classes
  - dynamic property allocation (whatever that is :)
support applications?
  - currently contains mostly libraries
  - hard to make sure the applications is usable by others
  - web page of useful scripts using the libs
  - demo with working examples
Documentation
  - currently in LaTeX
  - please contribute sample scripts
  - build a tutorial from questions on the mailing list
  - use Zope to have interactive examples
  - use Wiki (from extreme programming) for collaborative docs
Regression code
  - how to contribute?
  - what's the framework?
$$ for development?
Web site redesign
  - Gary volunteers (thanks!)
  - web should contain docs for available features
  - front page should address likely questions
More Documentation
  - Robert as QA for Brad's tutorial scripts
  - Rebecca to QA docs