Can massively parallel

DNA sequencing paired with

ubiquitous utility computing save the world?

Will Spooner, CTO, Founder, Eagle Genomics Ltd William.spooner@eaglegenomics.com

Image: http://grayninja93.deviantart.com/art/Glow-125681900 CC-BY-NC-ND 3.0

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

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

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

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:

Image: http://grayninja93.deviantart.com/art/Armageddon-128461009 CC-BY-NC-ND 3.0

NGS - democratising genomics

$1000 genome~$0.01 Mbase (30x coverage)

The Cost of Big Data

Now Soon

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

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

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

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

©