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SaaS Science as a Service

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1 1 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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Science is different 3


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Science as a service 4


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6 Evolution of Biomedical researchers


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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


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


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


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10 Personal Genome and Clinical Business


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


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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


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


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14 14 Challenges for Biomedical researchers


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


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16 ``Cloud Computing’’ in PubMed


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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.


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18 Startup Companies


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Galaxy Cloud 21 http://www.biomedcentral.com/1471-2105/11/S12/S4


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Galaxy Cloud 22


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Parallel Algorithms Spectrum 23


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CloudBurst 24


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RNAseq Unified Mapper (RUM) 26


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Myrna 27


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Contrail 29


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What’s Next? Alternative expression Allelic expression Structural variation Epigenomics Metagenomics Biological data/text mining Hapotype/Hapomap K thousand genomes 30


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NGS economics 33


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NGS economics 34


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NGS economics on clouds 35 2 1 3 4


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Voila! RNA-Seq Data Analysis 36


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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


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39 Eating your own dog food


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Science as a service Service as a science 42


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Loose coupled interdisciplinary 43


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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


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THANK YOU 45


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