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Progress on the Genomics Virtual Laboratory - Andrew Lonie
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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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  • 1. Progress on the Genomics Virtual Laboratory Andrew Lonie1 & Michael Pheasant21 Victorian Life Sciences Computation Initiative, University of Melbourne 2 University of Queensland
  • 2. What is the Genomics Virtual Lab?NeCTAR funded nationallydistributed platform for genomics,built on the Research Cloud andRDSI
  • 3. What is the Genomics Virtual Lab?
  • 4. 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
  • 5. Workflow platforms
  • 6. Cluster-on-the-cloud
  • 7. Use the public GVL, or roll your own
  • 8. Building a GVL http://usecloudman.org Cloudman = Middleware for building, distributing and managing cloud-based platforms, especially Galaxy
  • 9. Building a GVL image
  • 10. Tutorials and workshops
  • 11. genome.edu.au
  • 12. 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)
  • 13. 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)

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