Grid-enabled Biochemical Pathway Simulator was a system developed that supported large-scale simulation of biochemical networks to allow insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. A paper describing this system is available here.

Pharming of microRNA (mRNA): in collaboration with the Department of Pathology at the University of Glasgow, the NeSC at Glasgow developed a collection of tools to support the processing of large scale, high throughput microRNA data sets (typically tens of millions of short sequences of known and unknown origins). These data sets included cancerous data samples that have been treated over particular time windows. Through monitoring the changes in abundance of these sequences in specific time windows, the project showed that targeting of the effectiveness of drugs could be better understood and new genetic information gleaned, i.e. new genes that may be responsible for the changes in microRNA abundance.

Drug Discovery Portal (DDP): the DDP project involved a collaboration with the pharmaceutical group at the University of Strathclyde that focused on the development of a drug discovery portal supporting a molecular modeling laboratory using quantum chemical and thermodynamic based approaches to drug design. This portal dramatically sped up computational problems of pharmaceutical relevance utilizing a virtual foot-printing technique designed to identify agents that target specific gene sequences through software that explores the fundamental role of water structure in ligand binding. New DNA targeting agents were developed by combining novel analytical methods for assessment of DNA binding with synthetic chemistry, NMR studies and molecular modeling. Computer-aided drug design was also employed in the rational design of small molecules aimed at characterising ligand-protein interactions. The work also incorporated the manipulation of EGFR crystal structure, rational drug design, synthetic chemistry and in collaboration with cell biology groups, examination of synthesised ligands in biologically relevant cell-based assays.

Scottish Bioinformatics Research Network (SBRN): was funded by Scottish Funding Councils and Scottish Enterprise ran to 2010. SBRN aimed to develop an advanced e-Infrastructure across Scotland for biomedical research including the development and roll out of a rich portfolio of bioinformatics applications. This project supports the both the HPC and data Grid aspects of this proposal including exploration and usage of resources such as the National Grid Service and data access and integration technologies.

Grid Enabled Microarray Expression Profile Service (GEMEPS): was funded by the UK BBSRC and completed in 2008. The focus of GEMEPS was on access to and usage of microarray data sets in a truly international setting. The GEMEPS project was based on collaboration between the University of Glasgow, Cornell University in the US and the Riken Institute in Japan. GEMEPS focused on access to and usage of microarray data sets, which have their own IP and commercial values.

Biomedical Research Informatics Delivered by Grid Enables Services project (BRIDGES): was funded by the UK Government Department of Trade and Industry and completed at the end of 2005. It’s focus was on the incremental development of a Grid infrastructure supporting the secure, transparent federation of biomedical databases within the framework of the large Wellcome Trust biomedical research project Cardiovascular Functional Genomics exploring genetic causes of hypertension and schizophrenia. BRIDGES developed an extensive e-Infrastructure for access to and usage a multitude of large-scale compute resources consisting of heterogeneous job scheduling systems including the UK National Grid Service and many other resources. BRIDGES also applied open source data access and integration technologies as well as commercial data integration technologies (IBM’s Information Integrator) for large-scale access to functional genomics data sets. Security considerations formed a cornerstone of BRIDGES and fine-grained authorisation infrastructures for compute and data grids were rolled out and successfully exploited.

An Analytical Platform for the Integration of VicHealth Indicators Survey and Spatial Objective Contextual Data (VicHealth) commenced in 2013 as part of the AURIN project. The VicHealth system provides seamless and secure access to unit level data from the Department of Health in Victoria through a unique location identity-protecting manner. A paper describing this solution is available here.

Development of an integrated, distributed clinical research database for spinal cord injury, Victorian Traffic Accident Commission (SpinalCare) commenced in 2012 and has now established a national database of information on individuals that have incurred a range of spinal injuries. This includes details such as accident information, hospital/treatment information and subsequent follow up information on the patients when they return to society and the challenges they face.

Security as a Service for the Cloud (SECaaS) was funded ($225k) by the National eResearch Collaboration Tools and Resources (NeCTAR) project in October 2014. The focus of this project was on encryption/decryption technologies for the Cloud that meets the needs and expectations of the clinical/post-genomic research community. This work also included the development and support of capabilities for secure data deletion, i.e. deleting data from the Cloud so that it can never be recovered. This work involved a close collaboration with CSIRO and the life science community at the University of Melbourne, and focused on extensions to the TrustStore security platform.

ARC LIEF Atmospheric integrated research on burdens and oxidative capacity (Airbox) has been funded by the Australian Research Council ($630k) in 2015. Airbox will provide a custom built shipping container that will provide mobile atmospheric chemistry observations. This will allow for state-of-the-art observations of composition, physical parameters and aerosols relevant for international environmental treaties on air-quality, mercury, ozone depleting substances and greenhouse gases. The PRESS team are responsible for the underlying IT infrastructures that will support scientific data capture, data transport (telemetry), data analytics and visualisation of the data on servers at the University of Melbourne. A challenge of this work is the remoteness of the locations and the lack of / restricted internet that is available in those remote locations, especially with the volume of data sets that will be captured.