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	English	Japanese
Codon usage	English	Japanese
Bacteria analysis system	English	Japanese
Learning Perl for genome analysis	English	Japanese
Using BioMOBY with G-language GAE	English	Japanese
Various Perl scripts	English	Japanese
REST Web Service for Genome Analysis	English	Japanese[[RESTGenomeAnalysisJapanese

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

\

\

\