====== 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 | [[IntroductionToG-languageEnglish|English]] | [[IntroductionToG-languageJapanese|Japanese]] | ^ GCskew Basics | [[TutorialGCskewEnglish|English]] | [[TutorialGCskewJapanese|Japanese]] | ^ GCskew Advanced | [[GCskewAnalysisEnglish|English]] | [[GCskewAnalysisJapanese|Japanese]] | ^ GCskew Developer's Guide | [[GCskewOdysseyEnglish|English]] | [[GCskewOdysseyJapanese|Japanese]] | ^ Codon usage | [[TutorialCodonUsageEnglish|English]] | [[TutorialCodonUsageJapanese|Japanese]] | ^ Bacteria analysis system | [[BacteriaAnalysisSystemEnglish|English]] | [[BacteriaAnalysisSystemJapanese|Japanese]] | ^ Learning Perl for genome analysis | [[LerningPerl|English]] | [[http://web.sfc.keio.ac.jp/%7Egaou/wiki/wiki.cgi?page=%B8%A6%B5%E6%B4%D8%CF%A2%BB%F1%CE%C1|Japanese]]| ^ Using BioMOBY with G-language GAE | [[BioMOBYEnglish|English]] | [[BioMOBYJapanese|Japanese]] | ^ Various Perl scripts | [[VariousPerlScriptsEnglish|English]] | [[VariousPerlScriptsJapanese|Japanese]] | ====== Manual ====== ^Main API | [[http://www.g-language.org/documentation/1.7.2/G.html#SYNOPSIS|English]] | ^SubOpt API | [[http://www.g-language.org/documentation/1.7.2/SubOpt.html#SYNOPSIS|English]] | ^Rcmd API | [[http://www.g-language.org/documentation/1.7.2/Rcmd.html#SYNOPSIS|English]] | ^Messenger API | [[http://www.g-language.org/documentation/1.7.2/G/Messenger.html#SYNOPSIS|English]] | ^Analysis Methods API | [[http://www.g-language.org/data/gaou/doc/asimo/odyssey.pdf|English]] | ^GUI | [[http://www.g-language.org/documentation/BAS.pdf|English (PDF)]] | ^GenomeProjector API| [[http://www.g-language.org/GenomeProjector/wiki/Documents#development_api|English]] | ====== Complete API ====== ^ Complete API (Pdoc)^ | [[http://www.g-language.org/documentation/1.8.13/|Modules of G-language Genome Analysis Environment 1.8.13]] | | [[http://www.g-language.org/documentation/1.8.11/|Modules of G-language Genome Analysis Environment 1.8.11]] | | [[http://www.g-language.org/documentation/1.8.10/|Modules of G-language Genome Analysis Environment 1.8.10]] | | [[http://www.g-language.org/documentation/1.8.4/|Modules of G-language Genome Analysis Environment 1.8.4]] | | [[http://www.g-language.org/documentation/1.8.3/|Modules of G-language Genome Analysis Environment 1.8.3]] | | [[http://www.g-language.org/documentation/1.8.2/|Modules of G-language Genome Analysis Environment 1.8.2]] | | [[http://www.g-language.org/documentation/1.8.1/|Modules of G-language Genome Analysis Environment 1.8.1]] | | [[http://www.g-language.org/documentation/1.7.8/|Modules of G-language Genome Analysis Environment 1.7.8]] | | [[http://www.g-language.org/documentation/1.7.6/|Modules of G-language Genome Analysis Environment 1.7.6]] | | [[http://www.g-language.org/documentation/1.7.2/|Modules of G-language Genome Analysis Environment 1.7.2]] | | [[http://www.g-language.org/documentation/1.7.1/|Modules of G-language Genome Analysis Environment 1.7.1]] | | [[http://www.g-language.org/documentation/1.6.9/|Modules of G-language Genome Analysis Environment 1.6.9]] | | [[http://www.g-language.org/documentation/1.6.7/|Modules of G-language Genome Analysis Environment 1.6.7]] | | [[http://www.g-language.org/documentation/1.6.4/|Modules of G-language Genome Analysis Environment 1.6.4]] | ====== Benchmark comparison with Bioperl ====== ^Benchmark | [[benchmark|English]] | ====== 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|English]] | [[http://www.g-language.org/old/paper/gl1.pdf|Japanese]]| \\ ^Inspire | [[Inspire|Japanese]] | ^Bluebird | [[Bluebird|Japanese]] | ^Skyline | [[Skyline|Japanese]] | ^Version2 Nismo | [[Nismo|Japanese]] | ^v2roadmap | [[v2roadmap|Japanese]] | ^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|Japanese]] | ===== 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|PubMed]]). > 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|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|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|PubMed]]). > This paper describes the REST/SOAP Web services of the G-language System. ====== Further Reading ====== ^Review Articles^^^ | Large-scale Modeling for Systems Biology | [[BIOforumEurope1|Japanese]] | [[http://www.g-language.org/data/gaou/doc/BIOforumEurope-54-55.pdf|English]]| | Visualizing Complex Omics Information | [[BioforumEurope2|Japanese]] | [[http://www.g-language.org/data/gaou/doc/BIOforumEurope-2008.pdf|English]]| ====== Old versions ====== * [[http://www.g-language.org/documentation.html|Old Page]] \\ \\ \\