UC, San DiegoDepartment of Medicine   Trey Ideker Lab      SCSN@UCLA       Dec. 13, 2009
Keiichiro OnoUCSD Dept. of Medicine   Trey Ideker Lab Research Associate /  Software EngineerE-mail: kono@ucsd.edu     Twi...
••••
•
•    • DNA =   (ATGC)
•    • DNA =          (ATGC)       •      DNA=
•    • DNA =          (ATGC)       •      DNA=    •         =
•    • DNA =          (ATGC)       •      DNA=    •         =    •    =
Bioinformatics
•    ‣
•    •    •        •   1981   Smith-Waterman Algorithm (           )    •        •   1986                           Leroy ...
•    •        •   1990   BLAST             •    •
•    •        •   EBI (European Bioinformatics Institute, UK), KEGG (Kyoto Encyclopedia of            Genes and Genomes, J...
•    • 2000    •       •   Ensembl       •   UCSC Genome Browser    •    • Y2H
•    •        •    •        • R / Bioconductor    •
•    •    •    •       / Run        •
GenBank DataYear   Base Pairs             Sequences              http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html1982...
•    •    •        PC
•    ••••
•    ••••
••    •
••    ★
•    (PPI)•••
BioGRID Human Interactome
••    PPI
•    ••    ••
Cytoscape
I/O             Import most standard   Import networks, attributes   WikiPathways      BiNoM                    BioNetBuil...
Cytoscape
••
•    • Human-curated reference pathways    • Large-scale PPI    • Annotation for components    • etc.       •
• NCBI• EBI• DBCLS
•••   API
•       DBCLS EBI•• BioHackathon   • Web Service API
BioHackathon2009 in Japan✤   End of March, 2009 in    DBCLS(Tokyo)/    OIST(Okinawa)✤   Roughly 70% of the attendees    we...
•••   TV
http://sourceforge.net/apps/mediawiki/bio2rdf/index.php?title=File:Bio2rdfmap_blanc.png
••    •        ?
•    •        ≠
••••
••    • Python / Ruby    • R / Bioconductor
••    •    •
••
http://www.cytoscape.org/    kono@ucsd.edu     Twitter ID: c_z
Thank You!
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
生命を理解する道具としての計算機  SCSN@UCLA
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生命を理解する道具としての計算機  SCSN@UCLA

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2009年末にUCLAで行ったSCSNでのプレゼンテーション資料。ライフサイエンス以外の分野の方向けに書かれています。

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  • 生命を理解する道具としての計算機  SCSN@UCLA

    1. 1. UC, San DiegoDepartment of Medicine Trey Ideker Lab SCSN@UCLA Dec. 13, 2009
    2. 2. Keiichiro OnoUCSD Dept. of Medicine Trey Ideker Lab Research Associate / Software EngineerE-mail: kono@ucsd.edu Twitter: c_z
    3. 3. ••••
    4. 4.
    5. 5. • • DNA = (ATGC)
    6. 6. • • DNA = (ATGC) • DNA=
    7. 7. • • DNA = (ATGC) • DNA= • =
    8. 8. • • DNA = (ATGC) • DNA= • = • =
    9. 9. Bioinformatics
    10. 10. • ‣
    11. 11. • • • • 1981 Smith-Waterman Algorithm ( ) • • 1986 Leroy Hood • • 1988 NCBI
    12. 12. • • • 1990 BLAST • •
    13. 13. • • • EBI (European Bioinformatics Institute, UK), KEGG (Kyoto Encyclopedia of Genes and Genomes, Japan) • • • BioPerl
    14. 14. • • 2000 • • Ensembl • UCSC Genome Browser • • Y2H
    15. 15. • • • • • R / Bioconductor •
    16. 16. • • • • / Run •
    17. 17. GenBank DataYear Base Pairs Sequences http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html1982 680,338 6061983 2,274,029 2,4271984 3,368,765 4,1751985 5,204,420 5,7001986 9,615,371 9,9781987 15,514,776 14,5841988 23,800,000 20,5791989 34,762,585 28,7911990 49,179,285 39,5331991 71,947,426 55,6271992 101,008,486 78,6081993 157,152,442 143,4921994 217,102,462 215,2731995 384,939,485 555,6941996 651,972,984 1,021,2111997 1,160,300,687 1,765,8471998 2,008,761,784 2,837,8971999 3,841,163,011 4,864,5702000 11,101,066,288 10,106,0232001 15,849,921,438 14,976,3102002 28,507,990,166 22,318,8832003 36,553,368,485 30,968,4182004 44,575,745,176 40,604,3192005 56,037,734,462 52,016,7622006 69,019,290,705 64,893,7472007 83,874,179,730 80,388,3822008 99,116,431,942 98,868,465
    18. 18. • • • PC
    19. 19. • ••••
    20. 20. • ••••
    21. 21. •• •
    22. 22. •• ★
    23. 23. • (PPI)•••
    24. 24. BioGRID Human Interactome
    25. 25. •• PPI
    26. 26. • •• ••
    27. 27. Cytoscape
    28. 28. I/O Import most standard Import networks, attributes WikiPathways BiNoM BioNetBuilder Droid formats via web servicesAnalysis Network Analyzer BiNGO mCode ClusterMaker jActiveModules VistaClaraInference MiMI Agilent Literature Search CytoProphet Expression Correlation Domain Graph Monet Mondrian GLay ClueGO CyOOG Cerebral BubbleVisualization RouterStructure & SFLD Loader StructureViz Cheminformatics DrugViz OmicsViz MetaNetterChemistry
    29. 29. Cytoscape
    30. 30. ••
    31. 31. • • Human-curated reference pathways • Large-scale PPI • Annotation for components • etc. •
    32. 32. • NCBI• EBI• DBCLS
    33. 33. ••• API
    34. 34. • DBCLS EBI•• BioHackathon • Web Service API
    35. 35. BioHackathon2009 in Japan✤ End of March, 2009 in DBCLS(Tokyo)/ OIST(Okinawa)✤ Roughly 70% of the attendees were developers, 30% were users (biologists)✤ Discuss and hack hot topics in bioinformatics software/ system
    36. 36. ••• TV
    37. 37. http://sourceforge.net/apps/mediawiki/bio2rdf/index.php?title=File:Bio2rdfmap_blanc.png
    38. 38. •• • ?
    39. 39. • • ≠
    40. 40. ••••
    41. 41. •• • Python / Ruby • R / Bioconductor
    42. 42. •• • •
    43. 43. ••
    44. 44. http://www.cytoscape.org/ kono@ucsd.edu Twitter ID: c_z
    45. 45. Thank You!

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