
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
Ruby on Rails - the famous MVC framework that made ruby popular
Merb - fast, lightweight MVC framework
Camping - 5k microframework
Sinatra - web development DSL
Ramaze - simple, light, and modular web application framework
Rack - Webserver interface
Distributed/Parallel Computing
Rinda - Linda parallel programming model in Ruby
rxgrid - Xgrid batch language
MPI Ruby - MPI bindings for Ruby
amazon-ec2 - Amazon EC2 API
Testing/Spec
Test::Unit - Unit testing in the Ruby standard library
Integration with other programming languages
JRuby - JVM ruby implementation
SWIG and Ruby - automatically generate C interfaces
Math/Statistics
Ruby-GSL - wrapper for the GNU Scientific Library
RSRuby- R statistics package in Ruby
Ruby NArray - similar to NumPy
Visualization/Graphics
Ruby Gnuplot - Gnuplot bindings
Ruby-Processing - The Processing language in Ruby
ruby-opengl - OpenGL bindings
Gruff - Graph API
Ruby-SVG - SVG Graphics
Machine Learning
Support Vector Machines in Ruby
Fast Artificial Neural Network library
Blogs about bioinformatics and Ruby
Saaien Tist - Jan Aerts, on bioinformatics and personal productivity
Bioinformatics Zen - Micheal Barton
Be sure to visit the Ruby for Bioinformatics room on FriendFeed for even more Ruby goodness.
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