Bio-IT World Asia 2013 - A Genomics Virtual Lab for Cancer Research

The Cancer Genomics Linkage Application has been presented at Bio-IT World Asia 2013

Video: Dr Mark Cowley talks about integrating, transforming and sharing "omics" data through workflows

Integrating, transforming and sharing data through workflows

Dr Mark Cowley from the Garvan Institute describes the benefits that the "Cancer Genomics Linkage Application" brings to researchers of the Australian Pancreatic Cancer Genome Initiative led by Professor Sean Grimmond and Andrew Biankin.

Video: Professor Andrew Biankin talks about integrating, transforming and sharing data to fight cancer

Integrating, transforming and sharing data to fight cancer

Professor Andrew Biankin from the Garvan Institute discusses the importance of empowering clinician and biologist researchers through the use of the Cancer Genomics Linkage Application to help them fighting cancer.

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.

The Project

The Cancer Genomics Linkage Application will enable the in-depth interrogation of cancer genomic datasets and allow the comparison to other genomic datasets by providing research Biologists and Clinicians with direct access to them through the Genomics Virtual Lab-Early Activity (GVL-EA).

This application will focus on the research being carried out by the Australian Pancreatic Cancer Genome Initiative (APGI) and aims to:

• Provide local access to a collection of selected public data sources e.g. the ICGC open access data, the 1000 Genomes (pilot 2 trios alignment)
• Enable researchers to transform and integrate these datasets along with user uploaded data via the Galaxy workflow system as part of the GVL-EA
• Provide tool wrappers for somatic mutation analysis
• Provide exemplar workflows using Galaxy that demonstrates how to integrate the tools and datasets
• Enable APGI researchers to share their workflows, making them available for re-use and to obtain a persistent identifier for publication
• Enable automatic generation of compliant RIF-CS for publication to Research Data Australia
• Assists researchers in accelerating their discovery process, reducing the time to publication
• Make these integration and analysis workflows available through the GVL-EA to the APGI researchers and the cancer research community more broadly