BioRuby

BioRuby provides an integrated environment for Bioinformatics (Biology Information science).

Object oriented scripting language Ruby has many features suitable for bioinformatics research, for example, clear syntax to express complex objects, regular expressions for text handling as powerful as Perl’s, a wide variety of libraries including web service etc.

As the Ruby syntax is simple and very clean, we believe that it is easy to learn for beginners, easy to use for biologists, and also powerful enough for the software developers.

In BioRuby, the developer can retrieve biological database entries from flat files, internet web servers and local relational databases.

These database entries can be parsed to extract information you need. Biological sequences can be treated with the fulfilling methods of the Ruby’s String class and with regular expressions.

The library can be integrated with tools like Blast, Fasta, Hmmer and many other software packages for biological analysis.

BioRuby supports major biological database formats and provides many ways for accessing them through flatfile indexing, SQL, web services etc. Various web services including KEGG API can be easily utilized by BioRuby.

Features:

• BioRuby shell
• API
• Documentation

Requirements:

• Ruby 1.8.7 or higher