Could genomics (plus NGS/Cloud) save the world?
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Can massively parallel
DNA sequencing paired with
ubiquitous utility computing save the world?
Will Spooner, CTO, Founder, Eagle Genomics Ltd [email protected]
Image: http://grayninja93.deviantart.com/art/Glow-125681900 CC-BY-NC-ND 3.0
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Famine Disease
Image: A. Cavanagh http://images.wellcome.ac.uk/ CC-BY-ND 2.0
Image: http://transformergirl.deviantart.com/art/Famine-257996482 CC-BY-NC-ND 2.0
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Image http://widescreenwallpapers.org/earth-wallpapers.html CC-BY-NC-ND 3.0
SyntheticLife
Gaia
Image http://ginosblog.com/2010/06/03/100-synthetic-life-is-a-babystep-away/ CC-BY-NC-SA
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Molecular Psychiatry advance online publication 30 August 2011; doi:10.1038/mp.2011.101
Scientific impact of genomics
Image: Sartr http://sartr.deviantart.com/gallery/?offset=96#/d1u0z75 CC BY-NC-ND 3.0
Phen
otyp
e As
soci
ation
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Genomics in plant breedingGermplasm/Pedigree
Phenotype/Genotype association
Phenotype Genotype
GenotypingPhenotyping
Assays
Breeding
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PhenotypicAssociation[biomarker]
Stratified Medicine
Right drug
Right patient
Right time
Pharmacogenomics
Genotypic
Transcriptomic
Epigenetic
Genomics in pharmacology
©
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Genetic DeterminismVs.
Missing Heritability
Image:
Image: http://grayninja93.deviantart.com/art/Armageddon-128461009 CC-BY-NC-ND 3.0
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NGS - democratising genomics
$1000 genome~$0.01 Mbase (30x coverage)
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The Cost of Big Data
Now Soon
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Image: PictureGirl http://pixdaus.com/single.php?id=256700 CC-BY-SA
Cloud Computing = Greater ScalabilityCloud Computing = Lower Cost
+ Greater agility+ More flexibility+ Faster time to market+ Improved business process
TSB project – “Cloud Analytics for the Life Sciences”• Eagle Genomics • University of Manchester• NGRL
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30,000 virtual Cores$1,300/HOUR
Cloud – democratising HPC
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Technological Divergence
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KnowledgeOpen Innovation
PublicationsOpen Access
MethodsOpen Source
ResultsOpen Data
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Doing Genomics Efficiently
• “Genome Content Management is the set of processes and technologies that support the creating, managing, and reporting of genomic data.”
Create
Man
ag
e
Report
Create
Report
Ext
end
Manage
Share
Reuse
TIMELINE: Bespoke……...Common Models……………Content Management Systems
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Genome Content Management Systems (G-CMS)
Wor
kflow
Orie
nted
Database O
riented
Open Source Proprietary
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Ensembl as a GCMS
Comparative Genomics
Functional Genomics
Variation
Assembly/GenesData Integration
Data Reporting
Data Analysis
Data Integration
Data Querying
Data QC
API
Leveraging Public Resources
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Genomics in research productivity
Apoptotic execution Phase
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Plant models for phytopharmacology
Image By: G. Nicolella http://luirig.altervista.org/cpm/albums/bot-002/normal_medicago-truncatula3637.jpg CC BY SA
Physcomitrella patens
Image By: Ralf Reski CC BY-ND
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Open Innovation
ExploreWork together to find a commonpurpose
NurtureBuild trust, shared language
ExploitTurn ideas intotangible benefits
CollaborateEnterpriseAcademiaGovernmentFoundations
©
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Collaborative Data Sharing Platform
Users
Customer 1
Sequ
ence
Ser
vice
Asset Layer
User Interaction Layer web terminal
Scientist Admin
Business LayerUser/Role
Management Data
ManagementApplication
ManagementSystem
MonitoringReporting/
Billing
Customer 1
Apps
Clusters
Data Files
Customer 2Depositor
Customer 3Collaborator
Customer 2
Data Files
Customer 3
Apps
Data Files
Servers Servers
Secu
rity
Laye
r
Public
Data Files
Apps
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Am
azon
EC2
Clo
ud
Customer SandboxEC2/AMIs
Condor
Ensembl
BioLinux
Open Architecture – Open Source
Gateway OpenAM Plugin
Web Server SEEKCycleCloud
MySQL SEEK Assets DB
Scientist Admin Depositor
OpenAM Server
OpenAM IdP (LDAP)
Customer IdP
SAM
LAu
then
ticat
e
Customer SandboxS3 Storage
Data FiData Fi
Data Files
Customer SandboxS3 Storage
Data FiData Fi
Data Files
CycleServer
Customer SandboxEC2/AMIs
Condor
Ensembl
BioLinux
HTTPSWeb
Auth
oris
e
Encrypt/Decrypt
SAML
Token Exchange
HTTPSWeb
HTTPSWeb
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Eagle Academic Collaborations
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Can genomics save the world?
• Genomics is revolutionising:– Basic research, – Plant breeding, – Healthcare.
• Genomics R&D is empowered by:– NGS, – Cloud computing,
• Collaboration is key– Open knowledge/science,– Public datasets,– Open innovation.
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–In under a month (June 2011);• 10 e coli isolates sequenced,• 9 genome assemblies released,• 16 genome annotations released,•Over 50 analyses performed,• Resulting in 12 citable publications
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Eagle Genomics
Genome Content ManagementIntegrated, Analysed, Validated,
Except where otherwise noted, this work is licensed under the Creative Commons Attribution 3.0 License
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