Tools and Webapps for Public High-Throughput Sequencing Database

An introduction of our activity for public database for high-throughput sequencing, presented at #Illumina #BaseSpace Worldwide Developers Conference 2014 in Japan at #DBCLS

Transcript

1. %#$-4ʹ͓͚Δ/(4ʹର͢ΔऔΓ૊Έʹ͍ͭͯ Research Institute for Information and Systems Database Center for Life Science Tazro Ohta <t.ohta@dbcls.rois.ac.jp> ! prepared for Illumina's BaseSpace Worldwide Developers Conference in Japan October 28, 2014 5PPMT
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2. Tazro Inutano Ohta @inutano
3. Web Tools by DBCLS, for Deep Sequencing Raw Data Repository Search Sequence Search Tools Galaxy Pipeline Agenda For Developers: Programmable Options DBCLS SRA API G2-series API TogoWS
4. Web Tools by DBCLS, for Deep Sequencing Agenda
5. Web Tools by DBCLS, for Deep Sequencing Raw Data Repository Search DBCLS SRA <sra.dbcls.jp> DBCLS AOE <aoe.dbcls.jp> Sequence Search Tools GGRNA <ggrna.dbcls.jp> GGGenome <gggenome.dbcls.jp> Galaxy Pipeline DBCLS Galaxy <galaxy.dbcls.jp> Pitagora-Galaxy <pitagora-galaxy.org> Agenda
6. Raw Data Repository Search DBCLS SRA Statistics of Sequence Read Archive Extended Metadata Full-text Search Engine DBCLS AOE Statistics of ArrayExpress by EBI Interactive Visualization Faceted Search
11. Sequence Search Tools GGRNA Ultrafast Text Search for genes and transcripts Against all organisms in RefSeq Best for short nucleotide sequence search GGGenome Ultrafast Text Search for Ref. Genome Mismatches/gaps CRISPR/Cas Design Feature <coming soon!>
14. Galaxy Pipeline DBCLS Galaxy Public galaxy server + VMWare OpenID login Original Tutorial Videos Pitagora-Galaxy Portable pre-configured Galaxy VirtualMachine/Docker Container Monthly Galaxy Workshop in Tokyo
19. $ docker run -d -p 8080:80 inutano/pitagora-galaxy
20. For Developers: Programmable Options
21. For Developers: Programmable Options DBCLS SRA Data Retrieve Search API Quality API <coming soon> G2-series API TogoWS
31. via https://twitter.com/meso_cacase/status/519027645342707715
32. via https://twitter.com/bonohu/status/519030112147103744
39. via https://twitter.com/mishimahryk/status/524427733938352128
40. Web Tools by DBCLS, for Deep Sequencing Raw Data Repository Search Sequence Search Tools Galaxy Pipeline For Developers: Programmable Options DBCLS SRA API G2-series API TogoWS
41. Thank you, and Happy Hacking! http://speakerdeck.com/inutano