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Galaxy Australia: Bioinformatics tools without the scripting, and with reference data and compute included

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Slides from Gareth Price for the 14 Jun 2018 EMBL-ABR Webinar about Galaxy Australia.

Gareth, Head of Computational Biology at QFAB in Brisbane and Service Manager of the new and improved Galaxy Australia service presented on the general features of Galaxy, what’s changing nationally and why, and how researchers across Australia can benefit from the improved platform and service on offer.

A recording of the webinar is available here: https://youtu.be/5PBOoBo_ySM

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Galaxy Australia: Bioinformatics tools without the scripting, and with reference data and compute included

  1. 1. Galaxy Australia: Bioinformatics tools without the scripting, and with reference data and compute included Dr Gareth Price, Service Manager of Galaxy Australia (QFAB) Supported by Development partners
  2. 2. What is Galaxy
  3. 3. History (data and results) Tools
  4. 4. Interactive Window
  5. 5. Workflow Screenshot
  6. 6. Workflows ● Chain tools together into a workflow ○ Build “up front” / by design ○ Build from your history of successful data – results ■ Galaxy works out the journey your data took and auto configures the workflow ● Reusable on new data, simply trigger workflow on each new dataset and send to a new history (keeping your analyses cleanly separated) ● Shareable
  7. 7. The necessary backstory / context ● Generating genomic (genic, transcriptomic, methylation, variants, etc) has fallen almost year-by-year ● Inverse relationship to the amount of data being generated ● All of which has driven the need for more analysis resources
  8. 8. Why Galaxy and why Galaxy Australia? The Galaxy environment is design to enable researchers by providing an analysis platform that is: ● Sufficiently powered to answer their research questions ● Has the tools to analyse their data ● Has the references (genomes and annotations) to guide their analyses ● Has the capacity to share your data, results, visualisation and analysis pipelines (workflows) with collaborators ● Has the capacity to make analyses reproducible through design and execution of workflows
  9. 9. Galaxy Australia ● Galaxy Australia offers all the features of Galaxy (core*) as well as seamlessly integrated tools and references as requested by Australian researchers to support their work ● Galaxy Australia has recently been upgraded to: ○ incorporate new features ○ extended compute and quotas ○ more training resources ○ Over 600 tools and tool versions (for legacy analyses) ○ Over 200 reference genomes, indexed for rapid analyses ● Galaxy Australia service upgrade is part of the BioDEVL project (https://www.ands-nectar-rds.org.au/researchdomainprogram) * The concept of “core” and “Australian” will be explored in Simon’s presentation
  10. 10. DeVL project - Aims Aim 1 - rationalise and re-architect the public, managed GVL services: Galaxy-TUT Galaxy-MEL Galaxy-QLD RStudio including... https://usegalaxy.org.au
  11. 11. DeVL project - Aims Aim 2 - Harmonise look and feel with Other Global Galaxy Services including... https://usegalaxy.eu https://usegalaxy.org https://usegalaxy.org.au
  12. 12. DeVL project - Aims Aim 3 - Rationalise and expand existing Training Efforts ● Rationalise Australian developed Training Material: https://galaxy-au-training.github.io/tutorials/ ○ Includes new features to take advantage of the “here’s one I prepared earlier” option – context aware environment for training sessions that present users with results already generated for a particular tool and settings ● Establish a national network of Galaxy Trainers (via EMBL-ABR Nodes and others) ● Undertake at least 3 virtual/physical national training Galaxy events
  13. 13. We are here to help and support your research ● Helpdesk - help@genome.edu.au ● Learning - https://www.gvl.org.au/learn/
  14. 14. Stay in Touch ● GVL: https://www.gvl.org.au ● Galaxy Australia: Twitter https://twitter.com/galaxyaustralia ● Galaxy Australia Community https://www.embl-abr.org.au/galaxyaustralia ● And of course a final reminder: ○ Galaxy Australia https://usegalaxy.org.au
  15. 15. Using Galaxy Australia ● How much do I get ? ○ free to all researchers in Australia and your collaborators ● How do I start? ○ registration takes only a minute
  16. 16. DeVL Team Members Gareth Price (PM) - QFAB Simon Gladman - Melb Bionf Derek Benson - UQ-RCC Anna Syme - Melb Bioinf Igor Makunin - UQ-RCC Nuwan Goonasekera - Melb Bionf Christina Hall - Melb Bionf Helen van der Pol - Melb Bioinf

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