Nick’s Blog

I write a lot of code using the PYTHON Programing Language.  I just gave a very brief overview to a friend who has to learn it this summer. In the course of this lesson, it occurred to me that a lot of the bioinformatic resources that I use every day are not collected in one place.  So I’ve listed a couple of the most useful modules/packages below:

• BioPython
  • This package lets you interface with NCBI, parse datafiles (e.g. fastas, Genbank, blast output etc.), run blast queries, run clustalw, etc.
• SciPy
  • N-dimensional array manipulation
• MatPlotLib
  • Graphing.
• Python DB API
  • Database integration
• Google App Engine
  • Free webhosting of python cgi scripts.  It’s in beta.
• Django
  • Python Web Application Development package. It can be used in conjunction with Google App Engine.

Here are a few addition sites that I find useful:

• Â Python 2.5 Quick Reference
  • both html and PDF versions are available for free!
• TextMate
  • OS X text editor. It’s not free, but there is a student discount available
• Forklift
  • OS X ftp program. Also not free, but reasonably priced.