Tuesday 27 May 2014

ANDS AP24 BMRI Application - Final Product Report
May 28th, 2014
The AP24 project (Brain  and Mind Research Institute Application) has reached end of development and we are happy to announce the BMRI Application is available for the general public.
Introductory Product Information
One of the main problems in Brain and Mind Research Institute is that there is no such a tool that can efficiently and effectively collaborate the data captured from multiple tests.  The researchers need to collect, collate, and compile the data and the images together manually in order to perform analysis.  Another is the pre – processing of the MRI images. In order to read the image, research needs to pre – process the raw image from the scanner. Professor Jim Lagopoulos spends hours and hours a week just on helping the pre- processing because he is the only person who has the expertise to do it quickly.

These manual processes consume significant time and effort, replacing these by an automated process will be a huge success in the research area.

The system will improve the process efficiency by replacing the manual pre – processing to an automated pre- processing based on the researcher’s requirement.  Moreover, system integrates multiple sources of records and presents the summery of linked records according to user’s query, giving the user an overall view of related records. This automated functionality is previously not existed in this research filed of BMRI the University of Sydney.

The new process and functionality that has been brought by the application is highly welcomed by the researchers in BMRI, including:

  • Integrate, manage and store a diverse range of clinical research data.
  • Run MRI Scan pre-process through the process
  • Ingest existing research data
  • Enable users to manage access to research data.
  • Allow user to define and queries on research data.
  • Provide RIF-CS 1.4, Service, Party, Input Collection and Output Collection records to Research Data Australia.
  • Meets security standards.
  • Meets minimum accessibility requirements.

Project Aim

The aim of the project was to integrate various (a) imaging, (b) neurological & electrophysiological testing data and (c) clinical data for the purpose of providing a refined answer to complex research questions that was not previously possible using the separately existing (and expanding) data sets across the clinical research programs at BMRI making use of brain scans.

The project provided an integration tool for the multiple data sets and data points within those data sets and developed an analytical tool for interrogating the data in response to specific research questions. For example, researchers at the BMRI are trying to establish if there is a characteristic pattern that emerges from MRI structural imaging data and a specific electrophysiological component that predicts with some degree of accuracy a clinical phenotype, such as depression in young people.

The system developed through this project provides an integrated research data set to be expanded and used for future research projects. An additional objective was to integrate contributions to the data set from other clinical researchers and to make the larger data set available through research collaborations which was achieved by linking to the National Imaging Facility (NIF) via the DARIS application and has also enabled a University of Sydney wide imaging platform.

The outcomes of the project will provide data and an analysis platform for the development of information based diagnostic and treatment response algorithms for young people with major mental health problems like depression and psychotic disorders, as well as ageing subjects.

AP24 has provided a software solution covering the following functionality:
1.       Integrate large and sometimes disparate data sets held in SPSS and provide a platform to enable data transformation and analysis by authorised parties.
2.       Provide an analytical tool for interrogating the data in response to research questions (of the type discussed above).
3.       In cases where a research subject is under clinical care, and research findings may provide additional diagnostic support, provide mechanisms for communicating findings to the clinician.

Project outcomes

Prior to this project, researchers would manually collect, collate, and combine the data from the three information sources i.e. MRI, Neuropsychological, and EEG data by querying the various datasets for the specific requirements. The project has implemented an automated system that not integrates the data in one place, it also enables queries via metadata and attributes down to the field level to assist researchers in collecting data for analysis.


Instructional Product Information

The University of Sydney has chosen Daris as the solution software. The DARIS application utilises MediaFlux software and provides functions required by University of Sydney researchers.

The key functions required that Daris will be able to produces are:

  • Storage of MRI data
  • Storage of Neuropsychological data
  • Enable uses to manage access to specific data sets
  • Enable users to describe research data collections
  • Enable users to query the systems research data collection
  • Enable users to download research data
  • Enable the visualisation of research data
  • Make available RIF-CS 1.4 metadata available for harvesting via OAI-PMH.
  • Enable the creation of output collections
  •  
Solution components are broken down into the following:
  • Access control for authentication and authorization purposes.
  • Admin functionality is controlled by roles based permissions. Functional permissions management is a permissions controlled function that allows users to grant and revoke data access and to manage user roles.
  • Other function is to implement business functions. For example building form that allows users to add and update Neuropsychological data.
  • Reporting is a permissions controlled function that packages, compresses and makes datasets available for download by authenticated users.
  • File system storage will store the pre-processed data and its extended information like index.
  • Relational database will be used for system management configuration or user management information only.
  • Email Connector is the components that send appropriate emails to application users.
  • The OAI harvester makes RIF-CS 1.4 compliant metadata records .xml files public available for harvest Research Data Australia is a RIF-CS 1.4 .xml harvester.

Getting started

Please refer to the Developers Guide on instructions on how to download or build the tools.

Documentation

There are a number of manual and document resources available:
·         User Manual
·         Github repositories: Daris Wiki Home Page
·         Blog
·         Technical documentation:
Developers Guide- includes links to deployment and developer guides

Overview diagram

The following diagram outlines where the different tools fit within the research paths.




Product re-usability information

Imaging and clinical testing is not limited to neuroscience and mental health research, but extends to the University's research priority areas of cardiovascular disease, diabetes and obesity clinical research. As such the system will be developed to be disease independent and re-deployable for other systems (this will include the University of Sydney Charles Perkins Centre (formerly Centre for Obesity, Disease and Cardiovascular Disease (CODCD) or other research programs as required)  

The system has been designed to be able to be redeployed to other sites outside the University of Sydney. The source code is documented and packaged within http://nsp.nectar.org.au/wiki-its-r/doku.php?id=data_management:daris , enabling download and installation elsewhere.

The custom code that relates to the AP24 BMRI Application is code shared by a number of other institutions and has been sponsored by the Australian National Data Service (ANDS) http://ands.org.au/

During the project we have communicated our developments and progress with other Universities with a view gauging interest in redeployment and collaboration e.g. ANDS Distribution list and other meetings.

Contextual Product Information

All code is licensed under the GNU GPL v3 license - see LICENSE.txt in each code repository for license text. Documentation (contained in the Github wiki) is licensed under Creative Commons Attribution-Share Alike
Due to the extensive testing by the research stakeholders, the software is now robust, mature and fit for purpose. The ongoing maintenance of the software may occur in a number of ways, as appropriate:
  • Daris Software support is provided by the DARIS team under http://nsp.nectar.org.au/wiki-its-r/doku.php?id=data_management:daris:about 
  • MediaFlux support is provided by Arcitecta
  • The team at the BMRI and the University of Sydney may continue to enhance the software
  • Further enhancements and fixes may be done by the DARIS team or Arcitecta, under the support and maintenance agreement between the University of Sydney and Arcitecta. The sustainability of the product has been considered throughout the project and the software has been designed to maximise future maintainability:
  • The software has an extensive suite of automated unit tests that clearly describe the expected behaviour of the code.
  • This is augmented by a suite of integration tests created by the research stakeholders.
  • The code is open source so that other groups can contribute code back to the project.
The system has extensive documentation to explain the design and modules of the system and can be found at http://nsp.nectar.org.au/wiki-its-r/doku.php?id=data_management:daris
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Posted by Neal Anderson May 14th, 2014


ANDS AP24 BMRI Application – User Testing Report
User Testing Report
May 14th, 2014
User Testing has been completed on the AP24 application. Our user testing was completed by Associate Professor Jim Lagopoulos, Dr Daniel Hermens, and Django White, who have extensive experience in Neuroimaging (MRI), Neurophysiology, and Psychology, and are part of the Brain and Mind Research Institute at the University of Sydney.
The team used realistic data (in terms of content and size) for the testing of each data type individually and as data linkages, and their feedback was invaluable in helping produce a high quality solution. Read on for more info about their findings.
The Application
An overview of the application can be found on our wiki at Application Description and at the Wiki - About .
Source code can be found at:
Daris Source Code - this is the webapp that’s used to record experimental details and provide the feed to RDA.
We also have a User Manual, and Developers Guide. Check out the Wiki Home Page for further useful guides and documents.
Testing
Justin Chang has written a comprehensive test strategy documents that can be found at: ANDS AP24 BMRI Application Test Strategy

Associate Professor Jim Lagopoulos from BMRI said “The application will provide an environment for integrated research data sets that can be expanded and used for future research projects. The application will also allow the integration of data set from other clinical researchers and makes the larger data set available through research collaborations which was achieved by linking to the National Imaging Facility (NIF) and has also enabled a University of Sydney wide imaging platform.”

On top of the data integration and analysis, the application will also provide a platform for the development of information based diagnostic and treatment response algorithms for young people with major mental health problems like depression and psychotic disorders.

BMRI Research Fellow Daniel Hermens says “The application will improve the process efficiency by replacing the manual pre – processing to an automated pre- processing based on the researcher’s requirement.  Moreover, system integrates multiple sources of records and presents the summery of linked records according to user’s query, giving the user an overall view of related records. This automated functionality is previously not existed in this research field of BMRI the University of Sydney.”

The Brain and Mind Data Linkage application will be one of those tools that facilitate researchers understanding of variations in the brain’s structure, function and neurochemistry and consequently make a real impact on the way mental illnesses are diagnosed, treated and prevented.

Posted by Neal Anderson May 14th, 2014



New analytical tool speeds up research on youth mental illness

Mental illness is the number one health issue facing young Australians aged 12 to 15, affecting 26 percent of young Australian in any year. Mental illness may lead to depression, psychosis, alcohol and other drug issues and self-harm.  Mental illness developed during adolescence may stay with a person for life if the person doesn’t get help and the right treatment.

In partnership with Headspace Services (youth mental health http://www.headspace.org.au), researchers from the Brain and Mind Research Institute (BMRI) have set up the Healthy Brain Ageing program. This brings together patients, support groups and front-line carers with scientists and clinicians working in neurosciences and brain research to provide hope for those affected. 

A part of this research program involves collection, collating and analysis of dispersed clinic data, 3D MRI imaging and neurological & electrophysiological testing data sets for the purpose of providing a refined answer to complex research questions.

This automation of data linkages was not previously possible using the separately existing (and expanding) data sets making use of brain scans across the clinical research programs at BMRI. Collecting and collating data are time consuming. For example, in order to read the MRI image, researchers need to pre-process the raw MRI image from the scanner. Professor Jim Lagopoulos spends hours and hours a week just on doing the pre- processing because he is the only person who has the expertise to do it quickly.

A project “Brain and Mind Data Linkage" led by the BMRI and funded by the Australian National Data Service is changing that.  The project developed an integration tool for the multiple data sets and data points within those data sets, and an analytical tool for interrogating the data in response to specific research questions. For example, researchers at the BMRI are trying to establish if there is a characteristic pattern that emerges from MRI structural imaging data and a specific electrophysiological component that predicts with some degree of accuracy a clinical phenotype, such as depression in young people.

Associate Professor Jim Lagopoulos from BMRI said “The application will provide an environment for integrated research data sets that can be expanded and used for future research projects. The application will also allow the integration of data set from other clinical researchers and makes the larger data set available through research collaborations which was achieved by linking to the National Imaging Facility (NIF) and has also enabled a University of Sydney wide imaging platform.”

On top of the data integration and analysis, the application will also provide a platform for the development of information based diagnostic and treatment response algorithms for young people with major mental health problems like depression and psychotic disorders.

BMRI Research Fellow Daniel Hermens says “The application will improve the process efficiency by replacing the manual pre – processing to an automated pre- processing based on the researcher’s requirement.  Moreover, system integrates multiple sources of records and presents the summery of linked records according to user’s query, giving the user an overall view of related records. This automated functionality is previously not existed in this research field of BMRI the University of Sydney.”

The Brain and Mind Data Linkage application will be one of those tools that facilitate researchers understanding of variations in the brain’s structure, function and neurochemistry and consequently make a real impact on the way mental illnesses are diagnosed, treated and prevented.

The BMRI invites researchers to consider the possibilities of using AP24 for their own research projects. Associate Professor Jim Lagopoulos and BMRI Research Fellow Daniel Hermens, who helped develop AP24, say the application is not limited to clinical research, and can benefit other disciplines.

This project was supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund (EIF) Super Science Initiative.

Find out more.

Posted by Neal Anderson May 28th, 2014

Tuesday 13 May 2014

ANDS AP24 BMRI Application - User Acceptance Testing (UAT) Strategy



1.         Background

Mental health and Neuroscience research programs associated with the University of Sydney headspace Services (youth mental health http://www.headspace.org.au), and the Healthy Brain Ageing programs are undertaken at the Brain and Mind Research Institute. Clients of the headspace program are offered the option of participating in research studies, such as those examining the diagnosis and treatment for major health problems like depression and psychosis. Subjects for the Healthy Brain Ageing program are recruited through clinician referrals and direct applications. 

A number of these research studies involve health condition improvement programs (cognitive training, exercise, art, etc.). Research subjects from both studies are routinely scanned in a 3T MRI scanner and undergo at least a standard battery of neuropsychological (e.g. Cambridge Neuropsychological Test Automated Battery - CANTAB), and electrophysiological  testing (e.g. Mismatch negativity,  Auditory discrimination task, Emotional discrimination task, etc.).  The data obtained from the brain scans and the neuropsychological and electrophysiological tests generates the research projects’ raw data. 

This raw data is enriched by contextual information critical for use and reuse.  Research subjects themselves are contextualised by clinical data of essential value to the researcher.  Although existing tools support characterisation, management and sharing of scans and test results, there remains an important and unmet need for tools enabling the application and management of persistent links relating research data, contextual data and clinical data (de-identified in the case of human subjects).


Integration of these managed data types which would enable new types of statistical analyses (e.g. correlation, regression analysis) to be run across the combined research scans and clinical records (such as the case of comparing a research brain scan and the results of a clinical cognitive test).

Integration would also be of direct value to clinicians caring for patients who are also research subjects.  Research findings would be returned to referring clinicians, providing additional diagnostic support.

2.            People involved in the testing




Roles to be tested
System
Browser
·         Associate Professor Jim Lagopoulos
·         Dr Daniel Hermens
·         Justin Chang
·         John Twyman
·         Michael Homsey
·         Dr Will Ryder
project-administrator
DaRIS
Google Chrome 22.x,  IE 8.0, Firefox  12.x
·         Associate Professor Jim Lagopoulos
·         Dr Daniel Hermens
·         Justin Chang
·         John Twyman
subject-administrator
DaRIS
Google Chrome 22.x,  IE 8.0, Firefox  12.x
·         Associate Professor Jim Lagopoulos
·         Dr Daniel Hermens
·         Justin Chang
·         John Twyman
member
DaRIS


3                   Test Environment

3.1            People involved in the testing General Approach

The general approach for acceptance testing the ANDS AP24 BMRI Application is as follows:
  •          Architecta (vendor) are responsible for programmer unit testing;
  •          ICT project team are responsible for DaRIS for configuration testing;
  •          BMRI researchers, ICT project team, ICT Capability Solutions team for end user functional testing;
  •          Programmer unit testing will be hands-on and automated as per Architecta processes;
  •          End user functional testing will be hands-on;
  •          Test results will be documented by the respective teams;
  •          Test results will be collated by ANDS Ap24 project team;
  •          Testing sign-off is a responsibility of the Business Owners, Brain and Mind Research Institute (Michael Milne).


Business representatives who will participate in the UAT process will be required to prepare a set of test scenarios (to assist the business representatives a draft set of test scenarios has been written by the project team) that they will execute for each of the applications that they will test. These could be as simple as screen dumps of individual business processes or individual steps for each process requiring testing. These will be sent to the Test Manager prior to the UAT date for review and compilation.

There will be two test cycles for each project phase. The intention is that during the first cycle, all identified test scenarios will be executed. The second cycle allows for re-test of failed scenarios and some regression testing of the functions the new system changes will have an impact on.

UAT will require the identification and creation of test data. The project team and the business representatives prior to test execution will perform this task jointly.
The project team will provide user education to all participating testers prior to the commencement of the UAT. Such education is not a formal training session, but specifically designed for the execution of the UAT. It covers an overview of the new solution, usage of the new system, test methodology, incident management and technical support for UAT.

3.1.1          User Acceptance Test Environment

UAT will take place onsite at University of Sydney. The UAT Testing will be run on the Universities test bed against a full replica of the production database to ensure real world scenarios, data and compatibility.

3.2        Test Pre-Requisites

3.2.1          Login Accounts

The system administrator will be given full unrestricted access to the system to enable configuration of user roles during testing.

3.2.2          Data

Test data is as follows:
·         Youth Mental Health – DICOM T1 Weighted Structural Images (196 image series)
·         Youth Mental Health – NifTI T1 Weighted Structural *T1_n.nii
·         Youth Mental Health – NifTI T1 Weighted Structural *T1_n_r.nii
·         Youth Mental Health – NifTI T1 Weighted Structural *T1_n_r_brain.nii file
·         Youth Mental Health – DICOM Diffusion Tensor Images (4235 image series)
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI.nii_bvals
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI.nii_bvecs
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_nodif.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_nodif_brain_mask.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc.nii_ecclog
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc_tens_FA.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc_tens_L1.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc_tens_L2.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc_tens_L3.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc_tens_MD.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc_tens_MO.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc_tens_S0.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc_tens_V1.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc_tens_V2.nii
·         Youth Mental Health – NifTI Diffusion Tensor Images *DTI_ecc_tens_V3.ni
·         Youth Mental Health – DICOM T2 Weighted Functional MR Images (5460 image series)
·         Youth Mental Health – Folder of files *FMR.ica

3.2.3          Role permissions

project-administrator : user is allowed to administer the specific Project
subject-administrator : (pssd.project.subject.admin.<CID>) : user is allowed to administer Subjects in the specific project
member : user is a member (no admin and cannot see private meta-data on Subjects) of the specific Project

These roles are hierarchical; the project admin role contains the subject admin role contains the member role contains the guest role.


Prior to the execution of test cases, and on completion of development, a demonstration of the new application/system should be arranged. This meeting should be between the Developers, Project Manager, Test Team and User Acceptance Testers.
This education session should allow the testers to understand the application/system they are testing prior to the commencement of the actual Test Phase.

3.3        UAT Entry Criteria

UAT will commence if ALL the following criteria are met:
·          System Testing has been completed and ;
 No high severity or impact faults remain post system testing.
  •  Any medium/low severity or impact faults have agreed actions which will be resolved in a manner which will not impact User Acceptance testing.
  • Requirements/High Level Design or other relevant documents have been generated.
  • Sign-off of this Test Strategy has been completed by Project Team and Business Representatives.
  • Test Plan document which will include test cases has been completed, reviewed and signed off by the Project Manage.
  • Test environment has been successfully setup.
  • Any login accounts, required to complete User Acceptance testing, have been created
  • All testing tools and resources have been made available to relevant parties prior to commencement.
  • All training required has been provided to the Business Representatives team who will be testing new/modified systems.
  • Data, required to complete User Acceptance testing, has been migrated into the Test Environment.
  • Change Management methodologies in place and adhered to.
  • Tracking method/software in place and working, to monitor fault/issue tracking and resolution.
  • Access to development resources and personnel for issue resolution.
  • Access to Business Representative when required
  • Infrastructure support in place.

3.4        UAT Exit Criteria

  • UAT will be signed off if ALL the following criteria are met:
  • All UAT test cases are executed
  • All incidents identified during execution are logged
  • No Critical, High or Medium Severity errors remain open
  • Outstanding Low Severity errors scheduled for resolution
  • Business has provided a work around, for any outstanding issue(s) and has signed off on the release to UAT.
  • Test Completion Report completed and distributed to all relevant team members.


3.5        Sign off Procedures

UAT Sign Off Procedures

Upon completion of the UAT by all participating business units, the business representative from each business unit is responsible for completing and signing (if all test exit criteria are met) the Test Completion Report). This is to signify that the solution has been verified with respect to the business processes of their business unit and the new solution has been accepted.

Upon signing off on the UAT by all business units, all Test Completion Reports will be submitted to the Project Manager and used as a basis for their final endorsement on the overall solution.  Also the tested components will be released to Production environment via the Change Management Process.


Posted by Neal Anderson May 14th, 2014