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Slides from a talk at University of East Anglia (6th December 2011) looking at the recent advances in high-throughput genomics, and how these can be applied 'big issues' such as food security and disease. Particular attention is paid to the role of open science in reacting to critical situation.- Will Spooner, CTO.
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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]
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Famine Disease
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SyntheticLife
Gaia
Image http://ginosblog.com/2010/06/03/100-synthetic-life-is-a-babystep-away/ CC-BY-NC-SA
Molecular Psychiatry advance online publication 30 August 2011; doi:10.1038/mp.2011.101
Scientific impact of genomics
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Phen
otyp
e As
soci
ation
Genomics in plant breedingGermplasm/Pedigree
Phenotype/Genotype association
Phenotype Genotype
GenotypingPhenotyping
Assays
Breeding
PhenotypicAssociation[biomarker]
Stratified Medicine
Right drug
Right patient
Right time
Pharmacogenomics
Genotypic
Transcriptomic
Epigenetic
Genomics in pharmacology
©
Genetic DeterminismVs.
Missing Heritability
Image:
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NGS - democratising genomics
$1000 genome~$0.01 Mbase (30x coverage)
The Cost of Big Data
Now Soon
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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
30,000 virtual Cores$1,300/HOUR
Cloud – democratising HPC
Technological Divergence
KnowledgeOpen Innovation
PublicationsOpen Access
MethodsOpen Source
ResultsOpen Data
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
Genome Content Management Systems (G-CMS)
Wor
kflow
Orie
nted
Database O
riented
Open Source Proprietary
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
Genomics in research productivity
Apoptotic execution Phase
Plant models for phytopharmacology
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Physcomitrella patens
Image By: Ralf Reski CC BY-ND
Open Innovation
ExploreWork together to find a commonpurpose
NurtureBuild trust, shared language
ExploitTurn ideas intotangible benefits
CollaborateEnterpriseAcademiaGovernmentFoundations
©
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
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
Eagle Academic Collaborations
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.
–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
Eagle Genomics
Genome Content ManagementIntegrated, Analysed, Validated,
Except where otherwise noted, this work is licensed under the Creative Commons Attribution 3.0 License
©
