生命を理解する道具としての計算機 SCSN@UCLA
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This document summarizes information from a presentation on bioinformatics and systems biology. It discusses the history of bioinformatics from early sequence analysis tools to modern databases and pathways resources. It also describes Cytoscape as a tool for network analysis and visualization and mentions its ability to import networks from databases and perform analyses. Finally, it briefly discusses biohackathons as events for developers and users to collaborate on bioinformatics software.
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生命を理解する道具としての計算機 SCSN@UCLA
- 1. UC, San Diego Department of Medicine Trey Ideker Lab SCSN@UCLA Dec. 13, 2009
- 2. Keiichiro Ono UCSD Dept. of Medicine Trey Ideker Lab Research Associate / Software Engineer E-mail: kono@ucsd.edu Twitter: c_z
- 3. • • • •
- 5. •
- 6. • • DNA = (ATGC)
- 7. • • DNA = (ATGC) • DNA=
- 8. • • DNA = (ATGC) • DNA= • =
- 9. • • DNA = (ATGC) • DNA= • = • =
- 10. Bioinformatics
- 11. • ‣
- 13. • • • • 1981 Smith-Waterman Algorithm ( ) • • 1986 Leroy Hood • • 1988 NCBI
- 14. • • • 1990 BLAST • •
- 15. • • • EBI (European Bioinformatics Institute, UK), KEGG (Kyoto Encyclopedia of Genes and Genomes, Japan) • • • BioPerl
- 16. • • 2000 • • Ensembl • UCSC Genome Browser • • Y2H
- 17. • • • • • R / Bioconductor •
- 18. • • • • / Run •
- 19. GenBank Data Year Base Pairs Sequences http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html 1982 680,338 606 1983 2,274,029 2,427 1984 3,368,765 4,175 1985 5,204,420 5,700 1986 9,615,371 9,978 1987 15,514,776 14,584 1988 23,800,000 20,579 1989 34,762,585 28,791 1990 49,179,285 39,533 1991 71,947,426 55,627 1992 101,008,486 78,608 1993 157,152,442 143,492 1994 217,102,462 215,273 1995 384,939,485 555,694 1996 651,972,984 1,021,211 1997 1,160,300,687 1,765,847 1998 2,008,761,784 2,837,897 1999 3,841,163,011 4,864,570 2000 11,101,066,288 10,106,023 2001 15,849,921,438 14,976,310 2002 28,507,990,166 22,318,883 2003 36,553,368,485 30,968,418 2004 44,575,745,176 40,604,319 2005 56,037,734,462 52,016,762 2006 69,019,290,705 64,893,747 2007 83,874,179,730 80,388,382 2008 99,116,431,942 98,868,465
- 20. • • • PC
- 22. • • • • •
- 23. • • • • •
- 25. • • •
- 26. • • ★
- 27. • (PPI) • • •
- 30. • • PPI
- 31. • • • • •
- 32. Cytoscape
- 34. I/O Import most standard Import networks, attributes WikiPathways BiNoM BioNetBuilder Droid formats via web services Analysis Network Analyzer BiNGO mCode ClusterMaker jActiveModules VistaClara Inference MiMI Agilent Literature Search CytoProphet Expression Correlation Domain Graph Monet Mondrian GLay ClueGO CyOOG Cerebral Bubble Visualization Router Structure & SFLD Loader StructureViz Cheminformatics DrugViz OmicsViz MetaNetter Chemistry
- 35. Cytoscape
- 36. • •
- 38. • • Human-curated reference pathways • Large-scale PPI • Annotation for components • etc. •
- 39. • NCBI • EBI • DBCLS
- 40. • • • API
- 41. • DBCLS EBI • • BioHackathon • Web Service API
- 42. BioHackathon 2009 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
- 43. • • • TV
- 51. • • • ?
- 53. • • ≠
- 54. • • • •
- 55. • • • Python / Ruby • R / Bioconductor
- 56. • • • •
- 57. • •
- 58. http://www.cytoscape.org/ kono@ucsd.edu Twitter ID: c_z
- 59. Thank You!
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