SaaS Science as a Service

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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

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3. Science is different
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4. Science as a service
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5. 6
Evolution of Biomedical
researchers

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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

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The Trend of NGS
BRIEFINGS IN BIOINFORMATICS. VOL 11. NO 5. 484 ^ 498

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Illumina's Certified Service
Providers
www.illumina.com/services/cspro.ilmn

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Personal Genome and
Clinical Business

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http://news.sciencemag.org/scienceinsider/2010/06/uk-to-sequence-10000-genomes.html

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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
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http://www.genome.gov/27546261

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The Trend of NGS
ivory.idyll.org/permanent/lstein-ngs-capacity.png

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Challenges for Biomedical
researchers

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Solve It Using Cloud
Computing
http://genomebiology.com/2010/11/5/207

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``Cloud Computing’’ in PubMed

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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.

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Startup Companies

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19. Galaxy Cloud
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http://www.biomedcentral.com/1471-2105/11/S12/S4

20. Galaxy Cloud
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21. Parallel Algorithms Spectrum
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22. CloudBurst
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24. RNAseq Unified Mapper (RUM)
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25. Myrna
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27. Contrail
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28. What’s Next?
• Alternative expression
• Allelic expression
• Structural variation
• Epigenomics
• Metagenomics
• Biological data/text mining
• Hapotype/Hapomap
• K thousand genomes
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30. NGS economics
Biomedical
Researcher
Instrument
vendors
Sequencing
outsourcing
Analysis
outsourcing
Consultants
33

31. NGS economics
Biomedical
Researcher
Instrument
vendors
Sequencing
outsourcing
Analysis
outsourcing
ODM
Consultants
34

32. NGS economics on clouds
Biomedical
Researcher
Instrument
vendors
Sequencing
outsourcing
Analysis
outsourcing
Fabless
ODM
Consultants
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2
1
3
4

33. Voila! RNA-Seq Data Analysis
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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

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Eating your own dog food

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38. Science as a service
Service as a science
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39. Loose coupled interdisciplinary
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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
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41. THANK YOU
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