Carr, Vaughan

Catts, Stanley

Henskens, Frans

University of Queensland eSpace

An Example of eResearch: The 
Australian Schizophrenia 
Research Bank - ASRB
A/Professor Frans Henskens
A i t t D (IT) D t H d f S h l H d f Di i liss s an  ean , epu y ea  o  c oo , ea  o  sc p ne
Faculty of Engineering & Built Environment
School of Electrical Engineering & Built Environment
11 November 2009
3Schizophrenia
• A mental illness characterised by 
– Complex clinical symptoms
C i i d fi i– ogn t ve e c ts
– Subtle structural brain changes
• Prevalence of 4 per 1,000 sufferers
– But by its nature the illness it also affects family, friends & 
acquaintances
• Monetary cost to the community is ~$40 000 per patient per year      ,     
• E.g. the Russell Crowe movie A Beautiful Mind (Nash), recent tragic 
publicity
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
4
Research Into Schizophrenia  
• Investigation of life history, environment, etc
• Examination of brain morphology
– Until recently only possible after subject had died
– Now possible using MRI and fMRI technology
• Study of genetic characteristics   
– Typically involves analysis of blood samples
• Until recently involved disparate teams individually collecting and 
studying samples and data   
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
5Support for ASRB  
• Initial support for unified study provided by ARC Special Research Initiatives 
Grant: “A software grid for data-sharing associated with the NISAD/LONI Virtual 
Brain Bank” 2005/06 , 
• Major support provided by NHMRC Enabling Grant: “Australian Schizophrenia 
Research Bank”, 2006-2010
• Several smaller NHMRC grants 2007, 2008, 2009      
• Other financial support from The Pratt Foundation, Ramsay Healthcare, and 
Perpetual Trustees
• Administered and financially supported by Schizophrenia Research Institute 
(SRI)
• In-kind support INTERSECT: “ASRB – Web Interface and Tools”, 2009-2010
• Many other supporters (including John Singleton & Russell Crowe)
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
6
Purpose of ASRB  
• Shortage of patients and case-matched controls, characterised in terms 
of
Clinical–
– Cognitive
– Neuro-anatomical 
l tieva ua ons
• Will provide a bank of data (initially 2,000 subjects & 2,000 controls):
– Clinical & cognitive assessments
– Genetic data
– MRI brain scans
for use by national and international researchers
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
7Who Is ASRB?  
• Administered by SRI
• Led by scientists based at the University of Newcastle
• Collaboration with scientists at University of Melbourne, University of 
NSW, University of Queensland, University of Western Australia, 
Schizophrenia Research Institute
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
What Is ASRB Doing?
8
   
• Clinical Assessment Officers (CAOs)
– Conduct a comprehensive clinical assessment of each participant to 
collect 
• Socio-demographic & clinical history schedule
• Neurological, personality & cognitive function evaluations
Psychosis screening tool•   
representing a combination of the instruments currently used by 
prominent researchers in the field
• Technicians conduct MRI scan
• Qualified personnel extract blood samples
• Compliance with multi-level Ethics conditions is essential
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
How is ASRB Data Collected?
9
    
C O ( )• A s conduct the previously paper-based  assessments using 
purpose-built software on tablet computers
• A web portal allows upload of the data to a central database located in 
Newcastle
– The data is then removed from the tablet
– The ASRB web-site facilitates subsequent access to the data
• MRI data is transported to Newcastle on CD
– Processed to de-identify and normalised, then stored on the central 
server
• Blood samples are stored under refrigeration
• Complex rules govern right to access
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
Initial Technology
10
 
• PostgreSQL RDBMS on server and PCs
• Data described in XML
• CA software written in Java
– So can execute on Windows-based PCs and Unix-based server        
• JSP aligns software screens with database fields
• Transport Layer Security and Secure Socket Layer certificate ensures 
it f d t t fsecur y o  a a rans er
• Server access is controlled by Globus 4 grid
• Portal framework is Gridsphere with GridPortlets used to access the 
grid
• PURSe portlets abstract over certificate management for users
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
New INTERSECT Implemented
11
 -  
Application Software & Frameworks
• Java and PostgreSQL (v 8.3) as before
• Apache Tomcat servlet engine (http://tomcat.apache.org) 
• Liferay enterprise open source portal (http://www liferay com) - ASRB     . .   
Server
• Apache Pluto portal (http://portals.apache.org/pluto) - CAS Laptop 
Spring JEE application framework (http://www springsource org)•     . .
• Spring Security authentication and security framework 
(http://www.springsource.org) 
• Hibernate ORM persistence framework (http://www.hibernate.org)
• jQuery JavaScript and Ajax library (http://jquery.com)
• Several other Apache and other open source libraries and frameworks
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
New INTERSECT Implemented
12
 -  
Technologies & Techniques
• Dependency Injection (Inversion of Control) for run-time deployment
• MVI (Model-View-Controller) pattern for the UI
• Java Persistence API (JPA) for data persistence
• Java Architecture for XML Binding (JAXB) for XML processing
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
New INTERSECT Implemented Products
13
 -   
& Technologies for System Construction
• Eclipse IDE (http://www.eclipse.org)
• Subversion code revision control system (http://subversion.tigris.org/) 
• Apache Ant build tool (http://ant apache org)    . .  
• JUnit test framework (http://www.junit.org)
• EasyMock mock object library (http://easymock.org) 
• Hudson continous build and integration server (http://hudson-ci.org)
• Enterprise Architect UML modelling tool 
(http://www.sparxsystems.com.au)
• Atlassian Jira issue tracking system 
(http://www.atlassian.com/software/jira/)
• Atlassian Confluence enterprise Wiki 
(http://www.atlassian.com/software/confluence/)
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
Current State of Development
14
   
• New INTERSECT system:
– Testing with (copy of) real data will commence shortly        
– Deployment planned before end of year
• ASRB Data collected as of 6 weeks ago:
– 434 Cases: 288 male (66.4%); 146 female (33.6%)
– 248 Controls: 118 male (47.6%; 130 female (52.4%)
– Average age: 39.8 for cases; 37.7 for controls
– > 12 years education: 12.9% for cases; 15.4% for controls
Average age at onset: 23 0 for males; 25 2 for females–     .    .   
• INTERSECT demonstration follows this session
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
Use of ASRB for Research
15
    
• Integration of previous SRI Register and ASRB recruits to form ASRB           
Register
– Several approved studies currently recruiting using the Register
• From June 2009 CIs started accessing subsets of the data for conduct 
of studies
• Access will shortly open to other researchers
– Australian in July 2010
– International in July 2011   
23/11/2009
A presentation to eResearch Australasia  |  www.newcastle.edu.au
DISCUSSION
A presentation to eRsearch Australasia
11 November 2009
CRICOS Provider 00109J  |  www.newcastle.edu.au



An Example of eResearch: The Australian Schizophrenia Research Bank

http://espace.library.uq.edu.au/view/UQ:188379/Frans_Henskens_V4.pdf

An Example of eResearch: The Australian Schizophrenia Research Bank

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