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 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.

Text of Progress on the Genomics Virtual Laboratory - Andrew Lonie

  • 1. Progress on the Genomics Virtual Laboratory Andrew Lonie1 & Michael Pheasant21Victorian 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 GVLhttp://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 2012Prototype at Qld (UQ) and Vic (UoM) Galaxy UCSC browser + databases Bioinformatics cluster-on-the-cloud Initial tutorials and exemplarsJun 2013Production at Qld (UQ) and Vic (UoM), prototype @ other ResearchCloud nodesData coordination centres, data cataloguesDec 2013Additional workflows and tutorialsAdditional nodesJun 2014Operations (support centres - subscriptions) 13. Making the GVL possibleeResearch 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 InstitutesInitiative (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)