Published on May 10, 2014
11 SaaS Science as a Service Abner Huang <email@example.com> CSBB Lab., NTHU Dec. 14, 2011 Figure from GEN News Highlights: Jul 2, 2010
Science is different 3
Science as a service 4
6 Evolution of Biomedical researchers
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
8 The Trend of NGS BRIEFINGS IN BIOINFORMATICS. VOL 11. NO 5. 484 ^ 498
9 Illumina's Certified Service Providers www.illumina.com/services/cspro.ilmn
10 Personal Genome and Clinical Business
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
13 The Trend of NGS ivory.idyll.org/permanent/lstein-ngs-capacity.png
1414 Challenges for Biomedical researchers
15 Solve It Using Cloud Computing http://genomebiology.com/2010/11/5/207
16 ``Cloud Computing’’ in PubMed
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.
18 Startup Companies
Galaxy Cloud 21 http://www.biomedcentral.com/1471-2105/11/S12/S4
Galaxy Cloud 22
Parallel Algorithms Spectrum 23
RNAseq Unified Mapper (RUM) 26
What’s Next? • Alternative expression • Allelic expression • Structural variation • Epigenomics • Metagenomics • Biological data/text mining • Hapotype/Hapomap • K thousand genomes 30
NGS economics Biomedical Researcher Instrument vendors Sequencing outsourcing Analysis outsourcing Consultants 33
NGS economics Biomedical Researcher Instrument vendors Sequencing outsourcing Analysis outsourcing ODM Consultants 34
NGS economics on clouds Biomedical Researcher Instrument vendors Sequencing outsourcing Analysis outsourcing Fabless ODM Consultants 35 2 1 3 4
Voila! RNA-Seq Data Analysis 36
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
39 Eating your own dog food
Science as a service Service as a science 42
Loose coupled interdisciplinary 43
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
THANK YOU 45
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