TogoRecipes 120907
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© 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 Practical use case and applications Hiromasa Ono Hidemasa Bono 2012年9月7日金曜日
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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.
Transcript of TogoRecipes 120907
© 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･システム研究機構
Practical use case and applications
Hiromasa OnoHidemasa Bono
2012年9月7日金曜日
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 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
Survey of similar projects• myExperiment http://www.myexperiment.org
52012年9月7日金曜日
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
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
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 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)9
2012年9月7日金曜日
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
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)11
2012年9月7日金曜日
kaiko
122012年9月7日金曜日
