The Cancer Genomics Linkage Application will enable the integration and re-use of the cancer genomics data available from public repositories such as the International Cancer Genome Consortium (ICGC). This will be accomplished through the capability being developed by the “Early Activity” of the Genomics Virtual Laboratory (GVL-EA). It will enable researchers, such as Professors Andrew Biankin, John Mattick (Garvan Institute for Medical Research) or Sean Grimmond (Queensland Centre for Medical Genomics), to access genomic datasets of international importance and to integrate them with their own clinical and genomic datasets in order to explore, discover and validate key genomic abnormality that cause cancer. The product will further provide the mechanism for such researchers to publish and to make available their analysis for re-use by the community.

The product aims to provide the ability for biologists and clinicians to easily integrate their own research data with datasets from multiple data sources. The Integration of the datasets into a common location and enabling access and mining using best practice workflow tools will enable the Australian cancer researchers to accelerate their discovery processes and to be internationally competitive. Although this project will have a particular focus on pancreatic cancer research as carried out by the Australian Pancreatic Cancer Genome Initiative (APGI), the application can also support the wider cancer research community.

Download the application from here.

Sunday, 7 October 2012

Addressing users' needs

Our target users for this project are researchers of the Australian genomics community, in particular biologists and clinicians of the Australian Pancreatic Cancer Genome Initiative.

The challenges faced by these researchers are:

  • The manual process required to integrate their research data with other datasets
  • No availability of standardised analytical processes
  • The delay in transitioning from analysis to publication ready result

This project leverages the environment set up provided by the GVL-EA. The GVL-EA provides biologists and clinicians a ready to use analysis platform bypassing the time-consuming and complex process of setting up the underlying computational infrastructure. The "Cancer Genomics Linkage Application" will extend this environment by developing tools to manage data synchronisation; integration tools specific to the APGI research and provide some exemplar workflows using the Galaxy workflow system.

This application aims to increase the ease by which users can integrate their data with other data sources. It will provide mechanisms to publish data sources and user workflows to Research Data Australia (RDA) in order to increase search ability and re-use by the Australian research community.

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