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Bio-IT World Asia Conference 2013
A Genomics Virtual Lab for Cancer Research
Dominique Gorse
• 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