Documentations

Document Center

AJAX Document Center	http://ws.g-language.org/gdoc/

Double click on an entry to see its documentation.

Tutorials

Introduction to G-language GAE	English	Japanese
GCskew Basics	English	Japanese
GCskew Advanced	English	Japanese
GCskew Developer's Guide	[[GCskewOdysseyEnglish	English]]
Codon usage	[[TutorialCodonUsageEnglish	English]]
Bacteria analysis system	[[BacteriaAnalysisSystemEnglish	English]]
Learning Perl for genome analysis	[[LerningPerl	English]]
Using BioMOBY with G-language GAE	[[BioMOBYEnglish	English]]
Various Perl scripts	[[VariousPerlScriptsEnglish	English]]
REST Web Service for Genome Analysis	[[RESTGenomeAnalysisEnglish	English]]

Manual

Main API | http://www.g-language.org/documentation/1.7.2/G.html#SYNOPSIS | SubOpt API | http://www.g-language.org/documentation/1.7.2/SubOpt.html#SYNOPSIS | Rcmd API | http://www.g-language.org/documentation/1.7.2/Rcmd.html#SYNOPSIS | Messenger API | http://www.g-language.org/documentation/1.7.2/G/Messenger.html#SYNOPSIS | Analysis Methods API | http://www.g-language.org/data/gaou/doc/asimo/odyssey.pdf | GUI | http://www.g-language.org/documentation/BAS.pdf | GenomeProjector API| http://www.g-language.org/GenomeProjector/wiki/Documents#development_api |

Complete API

^ Complete API (Pdoc)^ | http://www.g-language.org/documentation/1.9.1/ | | http://www.g-language.org/documentation/1.9.0/ | | http://www.g-language.org/documentation/1.8.13/ | | http://www.g-language.org/documentation/1.8.11/ | | http://www.g-language.org/documentation/1.8.10/ | | http://www.g-language.org/documentation/1.8.4/ | | http://www.g-language.org/documentation/1.8.3/ | | http://www.g-language.org/documentation/1.8.2/ | | http://www.g-language.org/documentation/1.8.1/ | | http://www.g-language.org/documentation/1.7.8/ | | http://www.g-language.org/documentation/1.7.6/ | | http://www.g-language.org/documentation/1.7.2/ | | http://www.g-language.org/documentation/1.7.1/ | | http://www.g-language.org/documentation/1.6.9/ | | http://www.g-language.org/documentation/1.6.7/ | | http://www.g-language.org/documentation/1.6.4/ |

Benchmark comparison with Bioperl

^Benchmark | benchmark |

Architecture and Design

^The Development and Design of a Generic Genome Analysis Environment: The G-language system^^ | http://www.g-language.org/old/paper/gl.htm | http://www.g-language.org/old/paper/gl1.pdf| \ ^Inspire | Inspire | ^Bluebird | Bluebird | ^Skyline | Skyline | ^Version2 Nismo | Nismo | ^v2roadmap | v2roadmap | ^マシンへの負荷を考慮したプログラミング法 | マシンへの負荷を考慮したプログラミング法 |

Academic Publications about G-language System

• "G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining", Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M, //Bioinformatics//, 2003, 19(2):305-306 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12538262&query_hl=1&itool=pubmed_docsum).

This is the main article. Please cite this paper when you publish your research work using G-language System.

• "G-language System as a platform for large-scale analysis of high-throughput omics data", Arakawa K, Tomita M, //Journal of Pesticide Science//, 2006, 31(3):282-288(http://www.jstage.jst.go.jp/article/jpestics/31/3/282/_pdf).

This is a review describing G-language System and related software packages. Please also cite this article.

• "Computational Genome Analysis Using The G-language System", Arakawa K, Suzuki H, Tomita M, //Genes, Genomes and Genomics//, 2008, 2(1): 1-13 (http://www.g-language.org/data/gaou/doc/GGG-1-2008proof.pdf).

This review describes the algorithms implemented in G-language System, especially focusing on the identification of binding sites, analysis of genomic compositional skews, and codons.

• "G-language genome analysis environment with REST and SOAP web service interfaces", Arakawa K, Kido N, Oshita K, Tomita M, //Nucleic Acids Res.//, 2010, 38 Suppl:W700-705 (http://www.ncbi.nlm.nih.gov/pubmed/20439313).

This paper describes the REST/SOAP Web services of the G-language System.

Further Reading

^Review Articles^^^ | Large-scale Modeling for Systems Biology | BIOforumEurope1 | http://www.g-language.org/data/gaou/doc/BIOforumEurope-54-55.pdf| | Visualizing Complex Omics Information | BioforumEurope2 | http://www.g-language.org/data/gaou/doc/BIOforumEurope-2008.pdf|

Old versions

• http://www.g-language.org/documentation.html

\

\

\