Infrastructures Supporting Inter-disciplinary Research - Exemplars from the UK 

Infrastructures Supporting Inter-disciplinary Research - Exemplars from the UK Professor Richard O. Sinnott eResearch Director, University of Melbourne 9 th September 2010 [email_address]

Me Job description in a nutshell… make “e-” happen (Project Consultant on AURIN)

Track Record
National e-Science Centre (I, II, III)
Dynamic Virtual Organisations for e-Science Education
Biomedical Research Informatics Delivered by Grid Enabled Services
Grid Enabled Microarray Expression Profile Search
GridNet
Glasgow early adoption of Shibboleth
Joint Data Standards Survey
ESP-Grid
GridNet-2
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 (Supporting Multiple Shibboleth Attribute Authorities)
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
Completed On-Going

AURIN Investment Plan
Infrastructure
… to support ongoing data collection for urban research and the development of tools to interrogate those data
… problems of distributed data ownership, the diversity of formats
… considerations of privacy and the importance of maintaining granularity
… urban and built environment research community needs an infrastructure that provides better modelling and simulation tools that support integrated access to diverse datasets
… difficult to achieve in practice. Datasets created by organisations and researchers to meet their own specific needs
… propose to categorise principal methodologies, data types and types of sources, thus identifying key implementation issues
… strategic implementation streams used to define key data types and research approaches and to specify and develop infrastructure components necessary for realm of research
Many of these issues addressed by e-Research and e-Infrastructures

e-Research & e-Infrastructures
e=?
Electronic
Enabling
Empowering
Application of advanced ICT solutions to support research and researchers
Many software/middleware flavours
eResearch = High Performance Computing (HPC)?
Not always (I’d say mostly not!)
Successful Infrastructures should support
researchers and domain-specific research
often at the risk of being non-sexy!
seamless access to a heterogeneous variety of compute and data resources
Often domain/inter-domain specific – especially data!
single sign-on
Log in once and access resources without need for re-authentication and/or re-authorisation

e-Health Vision 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 …

e-Security
A A A A
A _ _ _ = authentication
= AAF?
Service provider 5. User accesses resource Web site/e-Journal Identity Provider Home Institution W.A.Y.F. Federation User AuthN Log-in once and roam
User points browser at Grid resource/portal (or non-Grid resource)
2. Shibboleth redirects user to W.A.Y.F . service 3. User selects their home institution 4. Home site authenticates user LDAP

_A _ _
Authorisation
Defining and enforcing rules on who can do what with what and when etc
Sites will have different rules/regulations
Virtual Organisations (VO)
Collection of distributed resources shared by collection of users from one or more organizations typically to work on common research goal
Provides conceptual framework for rules/regulations for resources to be offered/shared between VO-institutions and members
Different domains place greater/lesser emphasis on expression and enforcement of rules and regulations (policies)

AURIN Work Streams = e-VOs . . . {Resources} {Users} Org 1 {Resources} {Users} Org n VO VO specific agreements

_ A _ _
Role Based Access Control (attribute/identity/process…)
Basic idea is to define:
roles applicable to specific VO
roles often hierarchical
Role X ≥ Role Y ≥ Role Z
Manager can do everything (and more) than an employee can do who can do everything (and more) than a trainee can do
actions allowed/not allowed for VO members
resources comprising VO infrastructure (computers, data etc)
A policy then consists of sets of these rules
{ Role x Action x Target }
Can user with VO role X invoke service Y on resource Z?
Policy itself can be represented in many ways,
e.g. XML document, SAML, XACML, …
Standards on when/where these used (PEP) and enforced (PDP)
Should all be transparent to end users!

Privileges, Resources, Access Control and Trust Service provider Shib Frontend 5. Pass authentication info and attributes to auth Z function Grid Portal 6. M ake final AuthZ de cision Identity Provider Home Institution W.A.Y.F. Federation User AuthN AuthZ uid ? ? ? ? ? ? ? 1. User points browser at Grid resource/portal 2. Shibboleth redirects user to W.A.Y.F . service 3. User selects their home institution 4. Home site authenticates user and pushes attributes to the servic e provider LDAP LDAP

Proof of the Pudding
Inter-disciplinary research infrastructures
Data Management through e-Social Science (DAMES – www.dames.org.uk )
3 year ESRC funded project
Ends January 2011
Stirling (social science) and Glasgow (e-Support)
National e-Infrastructure for Social Simulation (NeISS – www.neiss.org.uk )
3 year JISC funded project
Ends April 2012
Centre for Spatial Analysis and Policy, University of Leeds
Manchester e-Research Centre, University of Manchester
STFC, Daresbury Laboratory
National e-Science Centre, University of Glasgow
Information Management Group, University of Manchester
OMII-UK, University of Southampton
Department of Applied Social Science, University of Stirling
Centre for Advanced Spatial Analysis - University College London

DAMES
Data research environments for social scientists
Occupational research environment (GEODE)
Educational research environment (GEEDE)
Ethnicity/minority research environment (GEMDE)
E-Health research environments (GEHDE)
Research into depression, self harm and suicide across Scotland
Does the number of people in a household have any effect on suicide rates?
Is there a correlation between age, sex, marital status, history of drug use (including prescribing drugs / anti-depressants) on suicide?
What is relation with access to parkland/green fields on depression?
What is optimal way to treat different forms of depression, e.g. drug treatments, therapists, …?
Does intervention-based cognitive behaviour therapy work?

DAMES GEHDE Data Space
Clinical data
Scottish Morbidity Records (SMR)
SMR01A General acute inpatient and day case discharges
SMR02 Maternity data
SMR04A Psychiatric/mental handicap admissions, residents, discharges
SMR06A Scottish cancer registrations
SMR99A Deaths
Social science/survey data
UK Census
1971 … 2001
Geospatial data
UK Boundary data
Changes over time to local authorities
License protected mapping data sets and tools

Demonstration
(video)

National e-Infrastructure for Social Simulation
Goals
Provisioning of variety of data sets/tools for social science research purposes
Key scenarios
Population demographics
changing population and impact on society
Health
smoking, obesity, …
Traffic
congestion charging, road pricing, promotion of non-vehicular alternatives to commuting
Sim City but with real data!
“ What-If” scenarios for users/policy-makers

NeISS Service Portfolio
Census 2001 – aggregate level data from ONS (via MIMAS)
PRM - creation of synthetic micro-populations for a city or region
• DSM - projects population of a city/region forward in time using representations
of key demographic processes, e.g. births, deaths, migration, marriage etc
TSM - spatial interaction service which assigns traffic behaviour (mode/route
choice) on basis of residential location/activity patterns in relation to fixed
transport infrastructure (from MOSES/GENESIS)
Aggregator - links individuals in a simulated population to individual level data
resources, e.g. BHPS
SurveyMapper – crowd sourcing solution from wider communities (from CASA/UCL)
FusionTool – service for auto-generation of missing data (from DAMES)
MapTube - allows to visualise spatial distributions using GIS shapefiles or 3 rd party
sources such as GoogleMaps (from CASA/UCL)

NeISS Tools Workflows

Demonstration
(video)

NeISS Infrastructure – Exemplars
Data Census tables (e.g. specific wards/output areas) used with PRM service to create synthetic population of individuals and households with basic demographic attributes
e.g. age, gender, marital status, ethnicity, quality of health, social group, housing
type, tenure…
Linking BHPS data to a synthetic population to estimate #smokers in Leeds

NeISS Infrastructure – Exemplars Each synthetically generated member of a population in a city, region or neighbourhood can be linked, e.g. to BHPS, by matching their demographic characteristics. From this process, additional characteristics can be assigned to the synthetic database using the profiles in the BHPS. The power of this lies in the fact that while the PRM generates in the order of 10 demographic and household attributes, the BHPS has over a thousand attribute fields. In this way, many spatial patterns can be newly inferred. Distribution of elderly people around Newcastle

NeISS Infrastructure – Exemplars DSM uses a series of sub-models representing key demographic transitions, e.g. marriage, migration, pro-creation, death and so forth Dynamic simulation showing proportional population change between 2001 and 2031 in Birmingham.

NeISS Infrastructure – Exemplars Three scenarios – congestion charging, road pricing and promotion of non-vehicular alternatives to commuting. For example, would policies on financial alternatives to leave a car at home and travel to work by bicycle actually work? Float idea to general public via tools like SurveyMapper – use results to gauge public response and inform policy makers, and as basis for calibration of simulation tools. Traffic scenarios

The Wider Context
Major (complementary) initiatives
$47m EIF Super Science National eResearch Collaboration Tools and Resources (NeCTAR)
$23m 2009/2010; $12m 2011/2012; $12m 2012/2013
Four key strands
National Servers Program
started
eResearch Tools Program
Sub-projects over 2-years from $500k-$1m
50% total costs
Research Cloud Program
Consultation exercise starting
Virtual Laboratories Program
Consultation exercise starting
Interim Director
Prof. Geoff Taylor, UoM Physics

The Wider Context
Super Science Research Data Storage Infrastructure
$50m – to be decided
Key data resources and data provider organisations
See spreadsheet
MANY other on-going efforts
AAF/ANDS/ASSDA/AuSCOPE/INSPIRE/SISS/…

Questions …?

Infrastructures Supporting Inter-disciplinary Research - Exemplars from the UK

by NeISSProject on Feb 10, 2011

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