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documents [2010/02/05 13:35]
admin
documents [2016/01/04 14:37] (current)
gaou
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 ^ AJAX Document Center | [[http://​ws.g-language.org/​gdoc/​]]| ^ AJAX Document Center | [[http://​ws.g-language.org/​gdoc/​]]|
 Double click on an entry to see its documentation. Double click on an entry to see its documentation.
- 
 ====== Tutorials ====== ====== Tutorials ======
 ^ Introduction to G-language GAE      | [[IntroductionToG-languageEnglish|English]] ​ | [[IntroductionToG-languageJapanese|Japanese]] | ^ Introduction to G-language GAE      | [[IntroductionToG-languageEnglish|English]] ​ | [[IntroductionToG-languageJapanese|Japanese]] |
 ^ GCskew Basics  ​ | [[TutorialGCskewEnglish|English]]  ​ | [[TutorialGCskewJapanese|Japanese]] ​ | ^ GCskew Basics  ​ | [[TutorialGCskewEnglish|English]]  ​ | [[TutorialGCskewJapanese|Japanese]] ​ |
-^ GCskew Advanced  ​ | <del>English</​del>​   | [[GCskewAnalysisJapanese|Japanese]] ​ | +^ GCskew Advanced  ​ | [[GCskewAnalysisEnglish|English]]   | [[GCskewAnalysisJapanese|Japanese]] ​ | 
-^ GCskew Developer'​s Guide  ​ | <del>English</​del>​   | [[GCskewOdysseyJapanese|Japanese]] ​ |+^ GCskew Developer'​s Guide  ​ | [[GCskewOdysseyEnglish|English]]   | [[GCskewOdysseyJapanese|Japanese]] ​ |
 ^ Codon usage  ​ | [[TutorialCodonUsageEnglish|English]]  ​ | [[TutorialCodonUsageJapanese|Japanese]] | ^ Codon usage  ​ | [[TutorialCodonUsageEnglish|English]]  ​ | [[TutorialCodonUsageJapanese|Japanese]] |
-^ Bacteria analysis system  ​ | [[BacteriaAnalysisSystemEnglish|English]]  ​ | <del>Japanese</​del> ​+^ Bacteria analysis system  ​ | [[BacteriaAnalysisSystemEnglish|English]]  ​ | [[BacteriaAnalysisSystemJapanese|Japanese]] 
-^ Learning Perl for genome analysis | <del>English</​del> ​| [[http://​web.sfc.keio.ac.jp/​%7Egaou/​wiki/​wiki.cgi?​page=%B8%A6%B5%E6%B4%D8%CF%A2%BB%F1%CE%C1|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]] | ^ Using BioMOBY with G-language GAE | [[BioMOBYEnglish|English]] | [[BioMOBYJapanese|Japanese]] |
 +^ Various Perl scripts  ​ | [[VariousPerlScriptsEnglish|English]]  ​ | [[VariousPerlScriptsJapanese|Japanese]] | 
 +^ REST Web Service for Genome Analysis | [[RESTGenomeAnalysisEnglish|English]]  ​ | [[RESTGenomeAnalysisJapanese|Japanese]] |
 ====== Manual ====== ====== Manual ======
 ^Main API | [[http://​www.g-language.org/​documentation/​1.7.2/​G.html#​SYNOPSIS|English]] | ^Main API | [[http://​www.g-language.org/​documentation/​1.7.2/​G.html#​SYNOPSIS|English]] |
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 ====== Complete API ====== ====== Complete API ======
 ^ Complete API (Pdoc)^ ^ Complete API (Pdoc)^
 +| [[http://​www.g-language.org/​documentation/​1.9.1/​|Modules of G-language Genome Analysis Environment 1.9.1]] |
 +| [[http://​www.g-language.org/​documentation/​1.9.0/​|Modules of G-language Genome Analysis Environment 1.9.0]] |
 +| [[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/​1.8.11/​|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/​1.8.10/​|Modules of G-language Genome Analysis Environment 1.8.10]] |
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 | [[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/​1.6.7/​|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]] | | [[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 ====== ====== Architecture and Design ======
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 ^v2roadmap | [[v2roadmap|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]] | ^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 ====== ====== Old versions ======
documents.1265376904.txt.gz · Last modified: 2014/01/18 07:44 (external edit)