Poster #RP105
BioRuby: samurai sword v.s. swissknife
Mitsuteru Nakao*, Naohisa Goto**, Nobuya Tanaka***, Toshiaki Katayama****
*Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu-sity, Chiba, 292-0818, Japan; **Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan; ***Bioinformatics Center, Institute of Chemical Resarch, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; ****Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
We have been developing an open source library to utilize various life science databases and bioinformatics applications. The BioRuby library is written in an object oriented scripting language Ruby, and by its nature the code becomes very clean and efficient.
Currently, BioRuby contains parsers for over 30 biological databases including Swiss-Prot and also extensible for other database format. Although the flat-file representation of the biological object is becoming obsolete as the relational databases and/or XML format is being widely used, parsing of the entry is still vital for bioinformatics analysis.
In this presentation, we will describe our framework to develop parsers and a benchmark focused on parsing of the Swiss-Prot database.
Functionality of the BioRuby is not limited to database parsing but covers biological sequence manipulation, execution of bioinformatics applications, 3D structures, biological pathways, and interfaces for various web services.
We will also represent our recent development including a new user interface, which is intended to be useful for biological researchers to utilize the power of BioRuby as their daily tool.