Walter Jessen

The Open Bioinformatics Foundation or O|B|F is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics. The mission of the O|B|F is to support the development of open source toolkits for bioinformatics, organize and run the Bioinformatics Open Source Conference (BOSC), and assist in the development and promotion of open source software for the life sciences. The foundation hosts code repositories for a number of open source projects, including four major programming languages that have bio* libraries (which can save a lot of headaches, not to mention coding time).

BioPerl: The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. The Bioperl server provides an online resource for modules, scripts, and web links. Pro: long history in bioinformatics, can do most anything. Con: awful syntax.

BioPython: The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. Pro: clean style, easy to read. Con: execution can be slow.

BioRuby: BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Pro: clean style, easy to read. Con: execution can be slow.

BioJava: The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data. Pro: great libraries, fast. Con: verbose and tedious to code.

I may have some MySQL and Oracle databases to mine for clinical parameter associations. I asked my social network on FriendFeed tonight which programming language would be best: Python, Ruby or Perl? The comments I received were consistent with what I’ve been reading: Python or Ruby.

It looks like I’ll be spending more time in the FriendFeed room Python for Bioinformatics.

What’s your favorite programming language and why?