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 24 th March 2011 rsinnott@unimelb.edu.au

“e-” Expensive!? Enabling Empo powering g 2.718… (th through gh rese search ch IT su suppo pport) t) Electronic Exabytes European? Everywhere Ethics It t is s not t abo bout t th the e- it t is s abo bout t th the r- Exascale 2

Track Record On-Going Completed • Meeting the Design Challenges of nanoCMOS • National e-Science Centre (I, II, III) Electronics (nanoCMOS) • Dynamic Virtual Organisations for e-Science Education • EU FW7 EuroDSD • Biomedical Research Informatics Delivered by Grid Enabled Services • EU FW7 AvertIT • GridNet, GridNet-2 • Breast Cancer Tissue Biobank • Grid Enabled Microarray Expression Profile Search • Data Management through e-Social Science • Glasgow early adoption of Shibboleth (DAMES) • Joint Data Standards Survey • NeSC Research Platform (NRP) • ESP-Grid • NeSC Information Network (NIN) • HPC Compute cluster award • ESF Network for Study of Adrenal Tumors • Sun industrial sponsorship • Scottish Health Informatics Platform for Research • OGC Collision (SHIP) • OMII-Security Portlets • National E-Infrastructure for Social Simulation • OMII-RAVE (NeISS) • Integrating VOMS and PERMIS for Superior Grid Authorization • Enhancing Repositories for Language and Literature • NCeSS Technical Management Researchers (ENROLLER) • CESSDA PPP • Proxy Credential Auditing Infrastructure for the NGS • Pharming of Therapeutic RNA • EU FW7 European Network for Study of Adrenal • Grid Enabled Occupational Data Environment Tumors Cancer Research Platform • Towards an e-Infrastructure for e-Science Digital Repositories • EU R4SME Diagnosis of Parkinsons Disease • Grid enabled Biochemical Pathway Simulator (DiPAR) • Virtual Organisations for Trials and Epidemiological Studies • EU European Platform for Study of Wolfram, Alstrom, • A European e-Infrastructure for e-Science Repositories Bardet Biedl • Modelling, Inference and Analysis for Biological Systems up to • Clinical Streaming Transcription Software the Cellular Level • Parathyroid Cancer VRE • Drug Discovery Portal • Advanced Grid Authorisation through Semantic Technologies • Multicenter prospective study of biochemical profiles ShinTau of monoamine-producing tumors (PMT Study) • Grid-enabled Virtual Safe Settings • Parliamentary Discourse • Scottish Bioinformatics Research Network (SBRN) • Scots Words and Placenames • Generation Scotland Scottish Family Health Study • AlstromUK VRE 3 • Australian Urban Research Infrastructure Network

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… 4

Inter-disciplinary e-Health BRIDGES Nucleotide sequences Nucleotide structures Gene expressions Protein Structures Protein functions Protein-protein interaction (pathways) Cell Security!!! + environmental, social, geographic … Cell signalling Tissues Organs Physiology Organisms Populations 5

BRIDGES Project 2 year project completed in 2005 with Glasgow, Edinburgh & IBM CFG Virtual Public ally Curated Data VO Authorisation Ensembl Organisation OMIM Glasgow SWISS - PROT Private Edinburgh MGI data HUGO Information RGD Private … Integrator data DATA Leicester HUB Private Oxford data Netherlands OGSA-DAI Private Private data Magna data London Synteny Vista Private Service Service data + + + 6

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 7

MagnaVista www.nesc.ac.uk 8

MagnaVista 9

GeneVista 10

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? competitors – $$$ • But from my end this was an extremely influential project • But this was/is not the point! 11

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 12

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 13

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 14

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! 15

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) 16

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EuroDSD Statistics Ro/erdam ¡ • Registry status 4.45% ¡ Cambridge ¡ 3.34% ¡ 2.23% ¡ 4.61% ¡ – 848 cases and moving in the Luebeck ¡ 6.52% ¡ 28.30% ¡ Pisa ¡ right direction! 6.68% ¡ Ghent ¡ 8.27% ¡ – Numerous major papers Lyon ¡ 23.85% ¡ 11.76% ¡ Glasgow ¡ published Stockholm ¡ • NEJM, Cell, … Birmingham ¡ – Many other groups now Kiel ¡ adopting this solution for 140 own DSD data mgt 120 • Argentina, Australia, Brazil, 100 Czech Rep, Estonia, Jordan, Cambridge 80 Glasgow Kiel Kuwait, Morocco, Poland, Luebeck Rotterdam 60 Birmingham Stockholm Portugal, Spain, Sudan, Ghent Pisa 40 Lyon Turkey, UK, USA, … (+ original EuroDSD countries) 20 – Support 24/7 access and 0 17/12/08 16/01/09 09/02/09 02/03/09 17/03/09 31/03/09 27/04/09 13/05/09 27/05/09 21/07/09 16/08/09 22/09/09 17/10/09 05/11/09 17/11/09 usage for over 2 years 18

e-Resourcing 19

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 tumour – Focu cus s on 4 ty type pes s of tu • Adrenocortical carcinoma (ACC) • Aldosterone Producing Adenoma (APA) • Non-aldosterone cortical adrenal adenomas (NAPACA) • Pheochromocytomas and related paragangliomas (Pheo) 20

ENSAT-CANCER 21