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SaaS: Science as a Service

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SaaS Science as a Service

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SaaS: Science as a Service

  1. 1. 11 SaaS Science as a Service Abner Huang <abnercyh@cs.nthu.edu.tw> CSBB Lab., NTHU Dec. 14, 2011 Figure from GEN News Highlights: Jul 2, 2010
  2. 2. 22
  3. 3. Science is different 3
  4. 4. Science as a service 4
  5. 5. 6 Evolution of Biomedical researchers
  6. 6. 7 Nature: Milestones in DNA 1977 DNA sequencing 1990 BLAST 2002 UCSC Genome browser 2004 Ensembl Figure from http://www.nature.com/milestones/miledna/timeline.html
  7. 7. 8 The Trend of NGS BRIEFINGS IN BIOINFORMATICS. VOL 11. NO 5. 484 ^ 498
  8. 8. 9 Illumina's Certified Service Providers www.illumina.com/services/cspro.ilmn
  9. 9. 10 Personal Genome and Clinical Business
  10. 10. 11 http://news.sciencemag.org/scienceinsider/2010/06/uk-to-sequence-10000-genomes.html
  11. 11. 12 NHGRI’s New Sequencing Projects • Genome Sequencing – Near $85 million in the first year • Mendelian Disorders – $12 million per year • Clinical Exploration – $10.3 million per year • Informatics Tools – $20 million for four years 12 http://www.genome.gov/27546261
  12. 12. 13 The Trend of NGS ivory.idyll.org/permanent/lstein-ngs-capacity.png
  13. 13. 1414 Challenges for Biomedical researchers
  14. 14. 15 Solve It Using Cloud Computing http://genomebiology.com/2010/11/5/207
  15. 15. 16 ``Cloud Computing’’ in PubMed
  16. 16. 17 Biomedical Institutes hug cloud computing • J. Craig Venter Institute released JCVI CLOUD BIO-LINUX • IBM eX5 Improves Next Generation Sequencing for Sanger Institute • ISB made Trans-Proteomic Pipeline (TPP) on clouds.
  17. 17. 18 Startup Companies
  18. 18. 19
  19. 19. Galaxy Cloud 21 http://www.biomedcentral.com/1471-2105/11/S12/S4
  20. 20. Galaxy Cloud 22
  21. 21. Parallel Algorithms Spectrum 23
  22. 22. CloudBurst 24
  23. 23. 25
  24. 24. RNAseq Unified Mapper (RUM) 26
  25. 25. Myrna 27
  26. 26. 28
  27. 27. Contrail 29
  28. 28. What’s Next? • Alternative expression • Allelic expression • Structural variation • Epigenomics • Metagenomics • Biological data/text mining • Hapotype/Hapomap • K thousand genomes 30
  29. 29. 32
  30. 30. NGS economics Biomedical Researcher Instrument vendors Sequencing outsourcing Analysis outsourcing Consultants 33
  31. 31. NGS economics Biomedical Researcher Instrument vendors Sequencing outsourcing Analysis outsourcing ODM Consultants 34
  32. 32. NGS economics on clouds Biomedical Researcher Instrument vendors Sequencing outsourcing Analysis outsourcing Fabless ODM Consultants 35 2 1 3 4
  33. 33. Voila! RNA-Seq Data Analysis 36
  34. 34. 38 IaaS Infrastructure as a Service PaaS Platform as a Service SaaS Software as a Service Cloud Service Models for Scientists www.spoutingshite.com/wp-content/uploads/2008/12/saas_and_cloud_computing.ppt
  35. 35. 39 Eating your own dog food
  36. 36. 40
  37. 37. 41
  38. 38. Science as a service Service as a science 42
  39. 39. Loose coupled interdisciplinary 43
  40. 40. Service science and cloud computing • HPC on cloud computing of NGS • Data Transfer Bottlenecks • Streaming Computing • Cost of Cloud Storage • Community Cloud Developing • App. Exchange of bioinformatics 44
  41. 41. THANK YOU 45

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