Kazuharu Arakawa　　Institute for Advanced Biosciences, Keio University

G-language Project: the last 10 years and beyondA presentation at the Bioinformatics Open Source Conference 2011

G-language Project2001 Apr. 26　g-language.org domain registred2001 Oct. 1　 beta public release

KBWS

REST/SOAP

Keio University Cornell University

Genome Analysis Environment (GAE)

“EMBOSS in Perl” - collection of 100s of programs, API for I/O, graphing, statisticsPerl Shell, BioPerl compatible

Genome Projector

Genome browser using Google Maps API

Pathway Projector

Pathway browser / mapping tool using Google Maps API

BookmarkletIntuitive query tool for EMBOSS, GAE services ( >500)Databases (NCBI Entrez, KEGG, EB-eye, Bio2RDF)

REST/SOAP web service for GAE

Keio Bioinformatics Web ServicesEMBASSY package for 50 web service tools

Arakawa et al. (2003) Bioinformatics

Arakawa et al. (2009) BMC Bioinformatics

Kono et al. (2009) PLoS One

Arakawa et al. (2010) NAR

Oshita et al. (2011) SCFBM

2001

2001 2004 2007 2009

Prelude coreOdyssay Packageg-language.org

v.1.0.0 asimo releaseGUI (Linux/Windows)

Bioinformaticsoriginal paper

NAR WS issueWS paper

JPSreview

GGGreviewISMB Best

Poster Award

2003

Keio Presidential Award

CBI ConferenceBest Poster Award

2002

SFC Award

2011

Mashup Awards 6thG-language Bookmarklet

Mashup Awards 4thGenome Projector

CGRSCFBM

Pathway ProjectorPLoS One

Genome Projector

BMCBioinformatics

Restauro-GGPB

GEM SystemBMC Bioinformatics

cDNAGPB

RCESBioinformatics

2006

GPACISB

marraydbISB

2005

MEGUISB

2008

Open-Bio.jpbook

2010

G-language Bookmarklet

v.1.1 releasedSkyline core

BioPerl compatibility

v.1.49 releaseWindows

support discontinued

G-language ShellInspire

Dynamic Loaderplug-in function

v.1.6 releaseMacOS X v.1.7 release

Bluebird/Infinity

v.1.8 releaseShell + Web Service enhancements

Genome Projector Pathway Projector

GEM System

KBWSREST/SOAPKNOB

SplitsX

ism

marraydb MEGU

E-Cell 3D

RCES

cDNA

Restauro 2Restauro-G

CGRGPAC

Mocog2s

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 Project: the last 10 years

KBWSSCFBM

• 4 papers for GAE, 11 for other tools• 6 awards• 83 citations (Google Scholar)• 4352 downloads (Sourceforge.jp)• 58 releases• 9 bi-lingual Tutorials（each quite lengthy）• 132 analysis programs, of which 49 are published• about 100 more APIs more for IO, DB, statistics, UI

Statistics

also distributed at bioinformatics.org, CPAN, KNOB, CD-ROM

• Research is a heuristic process: latency matters!• CPAN and BioPerl is great!• Availability of API for I/O, graphing, statistics allows you to concentrate on the important parts.

• Generic input type works quite nicely in workflows• Bookmarklet is an effective way to make small bioinformatics tools availble.

Lessons leant...

updates!

Genome Projector

Mash up Awards 4 - Google Award

Arakawa et al. (2009) BMC Bioinformatics

Zoomable Genome Browser with Multiple Viewspowered by Google Maps API

Wikipedia

Eijiro

Google

PubMed

EntrezKEGG/LinkDB

EB-eye

Bio2RDF

G-language

EMBOSS WWW

LinkedData

Semantic Web

Analysis

BLAST

Search with

G-language Bookmarklet: The Gateway to Semantic Web.http://www.g-language.org/wiki/bookmarklet

KBWS

• Internal ID converter (fetching mechanism of Linked Data) for more generic input handling

• pre-lapha http://rest.g-language.org/annotation/

• Environment that suggests possible next steps, or enrichment of certain data (GO, interactions, etc...)

• More statistics and visualization APIs

• Tighter integration of tools

and beyond...