Version 4 (modified by ktym, 12 years ago)

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BioHackathon 2009 meeting report

Work groups

G-language Genome Analysis Environment (G-language GAE) is a set of Perl libraries for genome sequence analysis that is compatible with BioPerl?, equipped with several software interfaces (interactive Perl/UNIX shell with persistent data, AJAX Web GUI, Perl API) [1-3]. The software package contains more than 100 original analysis programs especially focusing on bacterial genome analysis, including those for the identification of binding sites with information theory, analysis of nucleotide composition bias, analysis of the distribution of characteristic oligonucleotides, analysis of codons and prediction of expression levels, and visualization of genomic information. In this hackathon, the attendees from G-language Project implemented web-service interfaces for G-language GAE in order to provide higher interoperability. The RESTful web services provided at  http://rest.g-language.org/ provides URL-based access to all functions of G-language GAE, which is highly interoperable to be accessed from other online resources. For example, graphical result of the GC skew analysis of Escherichia coli K12 genome is given by  http://rest.g-language.org/NC_000913/gcskew. Another interface through the SOAP protocol provides programming language-independent access to more than 100 analysis programs. The WSDL file ( http://soap.g-language.org/g-language.wsdl) contains descriptions for all available programs in a single file, and can be readily loaded in Taverna 2 workbench [4] to integrate with other services to construct workflows.

References: 1. Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M, "G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining", Bioinformatics, 2003, 19(2):305-306. 2. Arakawa K, Tomita M, "G-language System as a platform for large-scale analysis of high-throughput omics data", Journal of Pesticide Science, 2006, 31(3):282-288. 3. Arakawa K*, Suzuki H, Tomita M, "Computational Genome Analysis Using The G-language System", Genes, Genomes and Genomics, 2008, 2(1): 1-13. 4. Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P, “Taverna: a tool for the composition and enactment of bioinformatics workflows”, Bioinformatics, 2004, 20(17): 3045-3054