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Progress on the Genomics Virtual Laboratory - Andrew Lonie
 

Progress on the Genomics Virtual Laboratory - Andrew Lonie

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The Genomics Virtual Laboratory (GVL) project, funded by NeCTAR, is building scalable infrastructure, workflow platforms and community resources for Australian genomics researchers. At this stage, the ...

The Genomics Virtual Laboratory (GVL) project, funded by NeCTAR, is building scalable infrastructure, workflow platforms and community resources for Australian genomics researchers. At this stage, the GVL
comprises: a prototype workflow management system based on the Galaxy framework, a bioinformatics toolkit (for command-line users), and a visualisation service based on the UCSC Genome Browser, all implemented on the NeCTAR Research Cloud; and a developing set of tutorials and exemplar workflows targetted at common high throughput genomics tasks. In this talk I will demonstrate GVL capabilities and discuss progress and the GVL roadmap.

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    Progress on the Genomics Virtual Laboratory - Andrew Lonie Progress on the Genomics Virtual Laboratory - Andrew Lonie Presentation Transcript

    • Progress on the Genomics Virtual Laboratory Andrew Lonie1 & Michael Pheasant21 Victorian Life Sciences Computation Initiative, University of Melbourne 2 University of Queensland
    • What is the Genomics Virtual Lab?NeCTAR funded nationallydistributed platform for genomics,built on the Research Cloud andRDSI
    • What is the Genomics Virtual Lab?
    • What did I promise today?Demonstrate GVL capabilities and discussprogress:1. scalable infrastructure on the Research Cloud a. workflow management system based on Galaxy b. a bioinformatics toolkit (for command-line users)2. a visualisation service (UCSC Genome Browser)3. a developing set of tutorials and exemplar workflows
    • Workflow platforms
    • Cluster-on-the-cloud
    • Use the public GVL, or roll your own
    • Building a GVL http://usecloudman.org Cloudman = Middleware for building, distributing and managing cloud-based platforms, especially Galaxy
    • Building a GVL image
    • Tutorials and workshops
    • genome.edu.au
    • Progress and timelinesDec 2012 Prototype at Qld (UQ) and Vic (UoM) ● Galaxy ● UCSC browser + databases ● Bioinformatics cluster-on-the-cloud ● Initial tutorials and exemplarsJun 2013 Production at Qld (UQ) and Vic (UoM), prototype @ other Research Cloud nodes Data coordination centres, data cataloguesDec 2013 Additional workflows and tutorials Additional nodesJun 2014 Operations (support centres - subscriptions)
    • Making the GVL possible eResearch Agencies ● Queensland Facility for AdvancedGo8 Universities Bioinformatics (QFAB) ● The University of Queensland ● Queensland Cyber Infrastructure ● The University of Melbourne Foundation (QCIF) ● Monash University ● Life Sciences Computation Centre ● The University of Sydney (LSCC) at the VLSCI ● The University of Western Australia ● Victorian eResearch StrategicMedical Research Institutes Initiative (VeRSI)● The Garvan Institute of Medical National Agencies Research ● NeCTAR, DIISRTE● Victor Chang Cardiac Research Institute ● CSIRO● Baker IDI Heart and Diabeties Institute ● EMBL Australia● Peter MacCallum Cancer Centre ● Bioplatforms Australia (BPA) ● Australian Genome Research Facility (AGRF) ● Australian National Data Service (ANDS)