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Kyoto University Team Wants to Put BioRuby OntheOpenSourceBioinformaticsMap


BioRuby, a project led by a team at Kyoto University, marks Japan’s first entry into the open source bioinformatics community.

Initiated as a means of supporting the KEGG (Kyoto Encyclopedia of Genes and Genomes) molecular interaction database, the project is now gaining support from a number of Japanese bioinformaticists who find BioRuby easier to work with than BioPerl or BioPython, according to Katayama Toshiaki, a BioRuby developer.

BioRuby is an object-oriented language, which makes the codes more simple and readable than BioPerl because all biological data is recognized as an object, according to Toshiaki. Neither Perl nor Python were designed as object-oriented languages.

Conceding that BioPerl is far more established than BioRuby and that many projects done in BioRuby could also be written in BioPerl, Toshiaki said the simplicity of BioRuby should appeal to bioinformaticists. He said the readability and maintainability of the code are easier than in BioPerl. In addition, Ruby offers a garbage collection feature to reclaim dynamically allocated storage, which is especially useful for the large amounts of data handled in bioinformatics, Toshiaki said.

The Kyoto team has used BioRuby to develop a data retrieval system in KEGG that is integrated with the local file access as well as web-based NCBI database access methods.

Toshiaki plans to submit a presentation on BioRuby at the Bioinformatics Open Source Conference and the Intelligent Systems for Molecular Biology Conference in Copenhagen, Denmark, this July.

“We want this project to expand internationally,” said Toshiaki.

— BT

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