Tools and Webapps for Public High-Throughput Sequencing Database

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

991f3366d9cc17386e6a66ef4abc6dbc?s=128

Tazro Inutano Ohta

October 29, 2014
Tweet

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 5PPMTBOE8FCBQQTGPS1VCMJD)JHI5ISPVHIQVU4FRVFODJOH%BUBCBTF
  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
  7. None
  8. None
  9. None
  10. None
  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!>
  12. None
  13. None
  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
  15. None
  16. None
  17. None
  18. None
  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
  22. None
  23. None
  24. None
  25. None
  26. None
  27. None
  28. None
  29. None
  30. None
  31. via https://twitter.com/meso_cacase/status/519027645342707715

  32. via https://twitter.com/bonohu/status/519030112147103744

  33. None
  34. None
  35. None
  36. None
  37. None
  38. None
  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