Bio-IT World Asia Conference 2013

A Genomics Virtual Lab for Cancer Research

Dominique Gorse

:: Introduction :: APGI

http://www.pancreaticcancer.net.au/

• Australian National Data Service • Established 2008 with $72M funding from the

federal government• Aim: “ANDS' task is to create the infrastructure to

enable Australian researchers to easily publish, discover, access and use research data.”

• “ANDS is building the Australian Research Data Commons (RDA): a cohesive collection of research resources from all research institutions, to make better use of Australia's research outputs.”

http://www.ands.org.au/index.html

:: Introduction :: ANDS

Aims

• Through the Genomics Virtual Lab– Integrate Cancer research data– Develop reusable workflows to assist in accelerating research– Reduce time from research publication– Deliver value to “research champions”

Will develop software that will enable researchers to access, integrate and

transform unique and valuable cancer genomics datasets and to analyse them

using the power of the Australian Genomics Virtual Lab

:: Cancer Genomics Linkage Project ::

Project Scope

• Develop functionality to “publish” GVL workflows to the RDA

• Provide software/infrastructure to enable integration/transformation of multiple datasets within the GVL environment

:: Cancer Genomics Linkage Project ::

UCSC Genome Browser

1- Data synchronisation

ICGC repositories GVL

2 - Data integration

Input Collection

Service description

Output Collection

3 - Development of Galaxy workflows enabling data integration and re-use

4. Publish to RDADOI creation for Galaxy Workflows

Galaxy

:: Cancer Genomics Linkage Project ::

:: Cancer Genomics Linkage Project ::

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BioMAJ

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Detailed RIF-CS for datasets

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Detailed RIF-CS for workflows

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http://ap27-cgla.blogspot.com.au/

:: Cancer Genomics Linkage Project ::

Project Features

1. Tools• QCMG’s QProfiler• QCMG’s QBamFilter• QCMG’s QSNP• Ensembl Variant Effector Predictor

2. Mirrored Data• ICGC Public dataset• Trio from the 1000 genome project• dbSNP• Drugbank

3. Workflows• QCMG workflow• Variant detection• RNAseq (VLSCI)

:: Project Examples ::

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

:: Acknowledgement::

This project is supported by the Australian National Data Service

The cancer genomics tools integrated in this application are developed by QCMG at the IMB, University of Queensland

:: APGI Funding::

www.qfab.org

:: The QFAB Scrum Development Team::

:: Scrum Product Owners::

Dr Mark CowleySenior Research Officer

Garvan Institute

Dr John PearsonSenior Bioinformatics Manager

QCMG - IMBDr Mingfang Wu

Senior Business AnalystANDS

Dr Jeff ChristiansenSenior Business Analyst