When I started working in a bioinformatics research lab I quickly discovered the wonderful dynamic language that is Perl. I’ve spent a couple of years with Mastering Perl for Bioinformatics somewhere on or around my desk. Perl itself was designed with text-processing and reporting in mind so naturally it’s become widely used when handling biological data.
So everything bioinformatics should be coded in Perl, right? A couple of years ago I might have agreed, but now I feel differently. My first “Perl, I’m leaving you.” moment came when I discovered the way that Rails does web programming. Ruby is the magic in Rails, but I soon discovered Ruby goes much beyond web frameworks. To quote Ezra:
“I came for the Rails, but I stayed for the Ruby”
I wanted to compile some links to show how an active community is positioning Ruby to be a powerful language for bioinformatics programming:
BioRuby - open source bioinformatics library
Web Frameworks
Distributed/Parallel Computing
Testing/Spec
Integration with other programming languages
Math/Statistics
RSRuby- R statistics package in Ruby
Visualization/Graphics
Machine Learning
Support Vector Machines in Ruby
Fast Artificial Neural Network library
[To be continued]
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