Practical use case          and applications               Hiromasa Ono               Hidemasa Bono                   © ライ...
22012年9月7日金曜日
32012年9月7日金曜日
Background     • LSQA Succession -> internationalization     • Variation of TogoTV (our movie tutorials)         –Cooking ...
Survey of similar projects     • myExperiment http://www.myexperiment.org                                                 ...
myExperiment     • PROS         –now a few workflows registered already         –RDF description of the public content is ...
TogoRecipes (temporal)     • Not workflow not pipeline. That’s recipe!!     • Recycling of used resources for       bioinf...
Implementation     • WordPress with SNS plugin (BuddyPress)                                                82012年9月7日金曜日
Recipes to be covered (1)     • Shell scripts for converting data formats.         –ex. s/r/n/g         –manipulate tab de...
Recipes to be covered (2)     • Application of UCSC data(UPBSB lecture)         –fetch genome annotation         –uncompre...
Recipes to be covered (3)     • Functional annotation of minor non-model       organism         –custom array: unique dupl...
kaiko                       122012年9月7日金曜日
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TogoRecipes 120907

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An extention of TogoTV for getting much more contributors and beneficiaries.
Advanced bioinformatics tips and tiny codes can be shared from this new feature, and the replication reports including corrections and suggestions can be deposited to TogoTV website.

Published in: Technology, Self Improvement
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TogoRecipes 120907

  1. 1. Practical use case and applications Hiromasa Ono Hidemasa Bono © ライフサイエンス統合データベースセンター/大学共同利用機関法人 情報・システム研究機2012年9月7日金曜日
  2. 2. 22012年9月7日金曜日
  3. 3. 32012年9月7日金曜日
  4. 4. Background • LSQA Succession -> internationalization • Variation of TogoTV (our movie tutorials) –Cooking recipe? (ex. Cookpad or Tasty kitchen) • Help using DBCLS Galaxy, or advanced use case for any other DB and webtools. –Reduce the COST of contributing the contents! - (“Wikipedia”lization, “community annotaiton”alization?) 42012年9月7日金曜日
  5. 5. Survey of similar projects • myExperiment http://www.myexperiment.org 52012年9月7日金曜日
  6. 6. myExperiment • PROS –now a few workflows registered already –RDF description of the public content is available –run with Taverna workbench • CONS –hard to interpret for novice –not compatible with TogoTV –run with Taverna workbench • small, but important tips not included 62012年9月7日金曜日
  7. 7. TogoRecipes (temporal) • Not workflow not pipeline. That’s recipe!! • Recycling of used resources for bioinformatics –Tips –tiny codes • Site management with –a focus on users posts and feedbacks –setting of Like! button 72012年9月7日金曜日
  8. 8. Implementation • WordPress with SNS plugin (BuddyPress) 82012年9月7日金曜日
  9. 9. Recipes to be covered (1) • Shell scripts for converting data formats. –ex. s/r/n/g –manipulate tab delimiter –perl/ruby –may be one liner? • Combination of EMBOSS programs on DBCLS Galaxy. –seqret (fetch sequences) -> emma (multiple alignment) –Extraction of upstream sequences (biomart) -> dreg (seek TFBS of your own) 92012年9月7日金曜日
  10. 10. Recipes to be covered (2) • Application of UCSC data(UPBSB lecture) –fetch genome annotation –uncompress -> extract column of your interest –countome analysis • Microarray data of your own –Search and fetch favorite data from NCBI GEO –JOIN those –hierarchical clustering, PCA, and gene enrichment analysis 102012年9月7日金曜日
  11. 11. Recipes to be covered (3) • Functional annotation of minor non-model organism –custom array: unique duplicated entry,id conversion –reference data (ensembl) –Tophit assignment -> JOIN! • RNA-seq (transcriptome sequencing) –copy FASTQ files –tophat -> cufflinks -> cummeRband –convert header description(combination of commands: head, tail, cat, mv) 112012年9月7日金曜日
  12. 12. kaiko 122012年9月7日金曜日

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