Expe perience ces s in Delivery of e-Infrastr structu ctures s - - PowerPoint PPT Presentation

Expe perience ces s in Delivery of e-Infrastr structu ctures s for Po Post- st-Genomic c Biomedi dica cal Rese search ch

Professor Richard O. Sinnott Director, eResearch 24th March 2011

rsinnott@unimelb.edu.au

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“e-”

Electronic

Empo powering g

(th through gh rese search ch IT su suppo pport) t)

Enabling Exabytes Expensive!? Ethics Everywhere European? 2.718…

It t is s not t abo bout t th the e- it t is s abo bout t th the r-

Exascale

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Track Record

• National e-Science Centre (I, II, III)
• Dynamic Virtual Organisations for e-Science Education
• Biomedical Research Informatics Delivered by Grid Enabled

Services

• GridNet, GridNet-2
• Grid Enabled Microarray Expression Profile Search
• Glasgow early adoption of Shibboleth
• Joint Data Standards Survey
• ESP-Grid
• HPC Compute cluster award
• Sun industrial sponsorship
• OGC Collision
• OMII-Security Portlets
• OMII-RAVE
• Integrating VOMS and PERMIS for Superior Grid Authorization
• NCeSS Technical Management
• CESSDA PPP
• Pharming of Therapeutic RNA
• Grid Enabled Occupational Data Environment
• Towards an e-Infrastructure for e-Science Digital Repositories
• Grid enabled Biochemical Pathway Simulator
• Virtual Organisations for Trials and Epidemiological Studies
• A European e-Infrastructure for e-Science Repositories
• Modelling, Inference and Analysis for Biological Systems up to

the Cellular Level

• Drug Discovery Portal
• Advanced Grid Authorisation through Semantic Technologies

ShinTau

• Grid-enabled Virtual Safe Settings
• Scottish Bioinformatics Research Network (SBRN)
• Generation Scotland Scottish Family Health Study
• Meeting the Design Challenges of nanoCMOS

Electronics (nanoCMOS)

• EU FW7 EuroDSD
• EU FW7 AvertIT
• Breast Cancer Tissue Biobank
• Data Management through e-Social Science

(DAMES)

• NeSC Research Platform (NRP)
• NeSC Information Network (NIN)
• ESF Network for Study of Adrenal Tumors
• Scottish Health Informatics Platform for Research

(SHIP)

• National E-Infrastructure for Social Simulation

(NeISS)

• Enhancing Repositories for Language and Literature

Researchers (ENROLLER)

• Proxy Credential Auditing Infrastructure for the NGS
• EU FW7 European Network for Study of Adrenal

Tumors Cancer Research Platform

• EU R4SME Diagnosis of Parkinsons Disease

(DiPAR)

• EU European Platform for Study of Wolfram, Alstrom,

Bardet Biedl

• Clinical Streaming Transcription Software
• Parathyroid Cancer VRE
• Multicenter prospective study of biochemical profiles
• f monoamine-producing tumors (PMT Study)
• Parliamentary Discourse
• Scots Words and Placenames
• AlstromUK VRE
• Australian Urban Research Infrastructure Network

Completed On-Going

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e-Experiences

• Many pr

projects cts

– All of th them have de delivered d e-Soluti tions s

– Someti times s pa painful bu but t always s ach chieved! d!

• Revoluti

tion?

– Some have bl blazed d a tr trail and d are now use sed d in ange ger

• Oth

thers… s…!?!?!

• Expe

perience ces s and d lesso ssons s learned d for futu ture…

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Inter-disciplinary e-Health

Nucleotide sequences Nucleotide structures Gene expressions Protein Structures Protein functions Protein-protein interaction (pathways) Cell Cell signalling Tissues Organs Physiology Organisms Populations

Security!!! + environmental, social, geographic …

BRIDGES

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BRIDGES Project

Synteny Service

Information Integrator OGSA-DAI

Magna Vista Service

VO Authorisation

+ + +

2 year project completed in 2005 with Glasgow, Edinburgh & IBM

Glasgow Edinburgh Leicester Oxford London Netherlands

Public ally Curated Data Private data Private data Private data Private data Private data Private data

CFG Virtual Organisation

Ensembl MGI HUGO OMIM SWISS - PROT

…

DATA HUB

RGD

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Grid Blast Interface

• Allows ‘genome scale’ blasting
• Transparently uses NGS,

ScotGrid, other GU clusters, Condor pools

• Many databases already

deployed across nodes

• No user certificates
• Fine grained security at

back-end

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www.nesc.ac.uk

MagnaVista

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MagnaVista

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GeneVista

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Buildi ding g Bridge dges! s!?

• Collaboration?
• Data providers

not factored in

• Revolution vs Evolution

– Both data/research space and the solution space

• Toothbrush culture?

– $$$

• But from my end this was an extremely

influential project

• But this was/is not the point!

competitors

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e-Research Support

• Different researchers/communities have

different eResearch needs

– Based on my experiences

– Inter-organisational collaborations – Data and data management – Security – High performance computing – Visualisation

» approximately in that order!

– Key to many eResearch endeavours is Ethics

• and Information Governance, Trust, Policy, Procedures, …

– Simply paying lip service here simply won’t cut it in the real world! » Disclosure Scotland

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Disorders of Sex Development

• Investigation of the molecular pathogenesis and

pathophysiology of Disorders of Sex Development (DSD) - EuroDSD – Extr treme Data ta Sensi siti tivity ty

• Typi

pica cally 10-12 ca case ses s in Sco cotl tland d pe per year

• Family issu

ssues, s, ch child d issu ssues, s, lega gal issu ssues, s, …

– 3-year pr project ct sta starte ted d May 2008

• Built on initial software prototypes developed by NeSC

Glasgow (on ~pro bono basis)

– Syste stems s have go gone th through gh inte ternati tional (inde depe pende dent) t) eth thica cal review

• now use

sed d for range ge of rese search ch areas s into to DSD

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EuroDSD Consortium

• Clinical Contr

tribu buto tors s

• Royal Children’s Hospital, Yorkhill, Glasgow
• University Hospital Schleswig-Holstein, Germany
• University of Cambridge, UK
• Erasmus University Rotterdam, Netherlands
• University Hospital of Pisa, Italy
• Karolinska Institute, Sweden
• Hospices Civils de Lyon, France
• Oth

ther rese search ch pa partn tners s

• Institute Pasteur, France
• University of Birmingham, UK
• University College London, UK
• Otto-von-Guericke-Universität Magdeburg, Germany
• Co-ordi

dinato tors/ s/pr project ct manage gers s

• GABO:mi mbH & Co. KG Germany

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Data Sharing and Ethics

• Clinica

cal da data ta sh sharing g di difference ces s acr cross ss Europe pe

• Ethics

– Committees / bodies – Structures and processes

• Consent

– Opt-in – Opt-out

• Data sharing

– Local only – National only – EuroDSD collaborators only – All international DSD researchers

• Ne

Need d for co compl plete tely di discr screti tionary da data ta sh sharing g mode dels s

• Driven by patient/parental consent
• Ethics, oversight, …

Designed with worst case scenarios in mind!

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Standard Operating Procedures & Associated Documentation

• Docu

cumenta tati tion

– The ESPE DSD Registry SOP [ PDF] – Data Flow within ESPE DSD Registry [ PDF] – ESPE DSD Registry information leaflet [ PDF] – ESPE DSD Register information leaflet children [ PDF] – Confidentiality Policy [ PDF] – Corporate Information Security Policy [ PDF] – System Level Security Policy (SLSP) [ PDF] – UG Data Protection Register details [ PDF] – Caldicott Recommendation [ PDF] – Appl to REC for approval of ESPE DSD Registry [ PDF] – UK ethics approval for ESPE DSD Registry [ PDF]

• (translated into international languages and used for

ethics across all countries/sites)

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EuroDSD Statistics

• Registry status

– 848 cases and moving in the right direction! – Numerous major papers published

• NEJM, Cell, …

– Many other groups now adopting this solution for

• wn DSD data mgt
• Argentina, Australia, Brazil,

Czech Rep, Estonia, Jordan, Kuwait, Morocco, Poland, Portugal, Spain, Sudan, Turkey, UK, USA, … (+

• riginal EuroDSD countries)

– Support 24/7 access and usage for over 2 years

28.30% ¡ 23.85% ¡ 11.76% ¡ 8.27% ¡ 6.68% ¡ 6.52% ¡ 4.61% ¡ 4.45% ¡ 3.34% ¡ 2.23% ¡ Ro/erdam ¡ Cambridge ¡ Luebeck ¡ Pisa ¡ Ghent ¡ Lyon ¡ Glasgow ¡ Stockholm ¡ Birmingham ¡ Kiel ¡

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e-Resourcing

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ENS NSAT-CANC NCER

• Europe

pean Ne Netw twork for Stu tudy dy of Adr drenal Tumours s (ENS NSAT – www.ensa sat. t.org) CANC NCER

– 6m E 6m Euro; uro; – 5-year pr project; ct; – sta starte ted d January 2011

• All IT th

through gh th the Universi sity ty of Melbo bourne

– Focu cus s on 4 ty type pes s of tu tumour

• Adrenocortical carcinoma (ACC)
• Aldosterone Producing Adenoma (APA)
• Non-aldosterone cortical adrenal adenomas

(NAPACA)

• Pheochromocytomas and related paragangliomas

(Pheo)

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ENSAT-CANCER

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ENS NSAT-CANC NCER

• Virtu

tual Rese search ch Environment t for all aspe spects cts of rese search ch asso ssoci ciate ted d with th adr drenal tu tumours s

• Secure web-based tumour databases; biobanking; clinical trials

– Two major drug trials » 2500 patients in each; Mitotane/Sunitinib for ACC/Pheo » Other trials already identified and will be supported

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ENSAT-CANCER

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Biobanking and Coding Systems

Plasma Free Metanephrines PFM Urine Free Metanephrines UFM Urine Deconjugated Metanephrines UDM Plasma Catecholamines PCA Urine Catecholamines UCA Urine Overnight Sample UON Plasma Chromogranin A CGA Blood DNA Sample (leukocytes) DNA Plasma Sample for Banking PBK Urine Sample for Banking UBK Tumor Tissue Sample TUM

• Na

Naming g / sta standa dardi disa sati tion of pr proto toco cols s for co countr tries, s, ce centr tres, s, pa pati tient t ide denti tifiers, s, sa sampl ples s

– Lack ck of sta standa dardi disa sati tion of LIMS

• DHL-like da

data ta tr track cking g

• Pati

tient t

– 1PF PFRPA1-003

• Sampl

ple

– 1PF PFRPA1-003TUM007

• (Pl

Plus s sta standa dardi disa sati tion of gu guide delines s

• n sto

storage ge, sh shippi pping, g, handl dling g etc) tc)

• Eth

thics cs appl pplied d for and d appr pproved d already dy

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• eRese

search ch ca can su suppo pport t rese search ch in th the field d

– meet stringent security demands of clinical research

• Many IT models exist

– There is no single solution that always applies

• I rarely start out with a preconceived IT solution

– Centralised, federated data models – Dependent/independent database – Push vs pull querying models

– Be fully aware of

• Ethics
• Information governance
• Community culture

– Carrot and stick!!!

• Need to proactively stimulate research pull

Conclusions

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Questions

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