Bosc2011 arakawa

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Bosc2011 arakawa

  1. 1. A presentation at the Bioinformatics Open Source Conference 2011
  2. 2. G-language Project Keio University Cornell University Genome Analysis Environment (GAE) Arakawa et al. (2003) Bioinformatics “EMBOSS in Perl” - collection of 100s of programs, API for I/O, graphing, statistics Perl Shell, BioPerl compatible Genome Projector Arakawa et al. (2009) BMC Bioinformatics Genome browser using Google Maps API Pathway Projector Kono et al. (2009) PLoS One Pathway browser / mapping tool using Google Maps API Bookmarklet Intuitive query tool for EMBOSS, GAE services ( >500) Databases (NCBI Entrez, KEGG, EB-eye, Bio2RDF)REST/SOAP REST/SOAP web service for GAE Arakawa et al. (2010) NAR Keio Bioinformatics Web Services Oshita et al. (2011) SCFBM KBWS EMBASSY package for 50 web service tools
  3. 3. G-language Project: the last 10 years Bioinformatics JPS GGG NAR WS issue ISMB Best original paper review review WS paper Poster Award RCES GEM System Bioinformatics BMC Bioinformatics Open-Bio.jp book CBI Conference Pathway marraydb cDNA GPAC MEGU Restauro-G Mashup Awards 4th Genome SFC Award Best Poster Award ISB GPB ISB ISB GPB CGR Projector Mashup Awards 6th KBWS Genome Projector Projector SCFBM PLoS One G-language Bookmarklet SCFBM Keio Presidential Award BMC Bioinformatics2001 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 v.0.x v.1.0.x v.1.1.x v.1.2.x v.1.3.x v.1.4~5.x v.1.6.x v.1.7.x v.1.8.x G-language Shell Inspire v.1.49 release Windows support discontinued v.1.6 release MacOS X v.1.7 release Bluebird/Infinity 2011 KNOB CGR REST/SOAP KBWS GPAC cDNA Restauro 2 v.1.1 released Restauro-G Skyline core BioPerl compatibility g2s Moco GEM System E-Cell 3D v.1.8 release v.1.0.0 asimo release Shell + Web Service enhancements GUI (Linux/Windows) SplitsX marraydb MEGU Dynamic Loader ism Genome Projector plug-in function Pathway Projector Prelude core G-language Bookmarklet Odyssay Package g-language.org RCES
  4. 4. Statistics also distributed at bioinformatics.org, CPAN, KNOB, CD-ROM
  5. 5. Lessons leant...
  6. 6. updates!
  7. 7. Genome ProjectorZoomable Genome Browser with Multiple Views powered by Google Maps API Mash up Awards 4 - Google Award Arakawa et al. (2009) BMC Bioinformatics
  8. 8. G-language Bookmarklet: The Gateway to Semantic Web. http://www.g-language.org/wiki/bookmarklet EMBOSS KBWS Wikipedia G-language Eijiro Google Bio2RDF PubMed EB-eye KEGG/LinkDB Entrez BLAST
  9. 9. and beyond...

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