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.

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
2012年9月7日金曜日

3. 3
2012年9月7日金曜日

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?)
4
2012年9月7日金曜日

5. Survey of similar projects
• myExperiment http://www.myexperiment.org
5
2012年9月7日金曜日

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
6
2012年9月7日金曜日

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
7
2012年9月7日金曜日

8. Implementation
• WordPress with SNS plugin (BuddyPress)
8
2012年9月7日金曜日

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)
9
2012年9月7日金曜日

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
10
2012年9月7日金曜日

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)
11
2012年9月7日金曜日

12. kaiko
12
2012年9月7日金曜日