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
Documentation
There are a number of
manual and document resources available:
·
Technical documentation:
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
Posted by
Neal Anderson May 14th, 2014
