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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
22
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
11
http://news.sciencemag.org/scienceinsider/2010/06/uk-to-sequence-10000-genomes.html
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
19
Galaxy Cloud
21
http://www.biomedcentral.com/1471-2105/11/S12/S4
Galaxy Cloud
22
Parallel Algorithms Spectrum
23
CloudBurst
24
25
RNAseq Unified Mapper (RUM)
26
Myrna
27
28
Contrail
29
What’s Next?
• Alternative expression
• Allelic expression
• Structural variation
• Epigenomics
• Metagenomics
• Biological data/text mining
• Hapotype/Hapomap
• K thousand genomes
30
32
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
40
41
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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