An introduction to the Galaxy platform for computational biology – with real-world hands-on demonstration

Background: Galaxy is a scientific workflow platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. By providing a graphical, web-based interface for running bioinformatics tools and pipelines, Galaxy removes the need to learn complex command-line syntax or the need to interact with computational job management systems. Galaxy also makes your analyses reproducible by maintaining a replicable history of analysis steps, and makes your research more transparent by allowing you to share your analyses with others. Here we will be showcasing the features of Galaxy on the Galaxy Australia service, usegalaxy.org.au. Login is open to all and only requires an email to access the full resources of Galaxy Australia.

Workshop content: The workshop will be run in two halves, an overview of the Galaxy platform, using Galaxy Australia as the example, then a practical demonstration of DNA sequence variant identification. We will start with the basics of Galaxy, by providing a run through of the interface, demonstrate how to get private and public data into Galaxy, and perform a common type of analysis using popular software tools. We will then build on this base to create a more complex workflow, publish this workflow and perform a more complex analysis, using an exemplar variant calling pipeline. We will also discuss the options available for installing and using Galaxy, including freely available public servers.

Target audience: System Administrators and researchers with an interest in carrying out bioinformatics analysis, either as a core service for an institute and for individual research questions. Attendees should bring a laptop to participate in the variant calling demonstration. The only required software is a web browser (Chrome preferred), both Mac and Windows supported.

Learning Outcomes: Attendees will learn how to:

  1. Access, login and use Galaxy to perform an analysis
  2. Import and Export of data
  3. Design and execution of chained tools / workflows
  4. Import / Export
  5. Sharing of an analysis with a collaborator
  6. Perform a series of analyses on a research topic – here will be DNA sequence variant identification

Simon Gladman1*, Igor Makunin2,4, Helen van de Pol1, Christina Hall1, Nuwan Goonasekera1, Andrew Lonie1, Nigel Ward3, Jeff Christiansen2,3, Gareth Price4*

  1. Melbourne Bioinformatics, University of Melbourne, Melbourne, Australia
  2. RCC-University of Queensland, Brisbane, Australia
  3. QCIF, Brisbane, Australia
  4. QFAB@QCIF, Brisbane, Australia
  • These authors will be presenting the Workshop

Simon Gladman – Simon Gladman is a bioinformatician at Melbourne Bioinformatics (part of the University of Melbourne.) Simon is one of the administrators of Galaxy Australia and has been involved in the Galaxy project since 2012. He is also part of the Galaxy Training Network, the Galaxy Tools IUC and the usegalaxy.* project. He has over ten years of experience teaching workshops and other training, regularly using Galaxy, for various audiences including biologists, bioinformaticians, students and other interested parties.

Gareth Price– Gareth Price is Service Manager of Galaxy Australia and Head of the Computational Biology team at QFAB. At QFAB Gareth helps translate researcher’s biological queries into the systemic informatics language required for analysis. Gareth’s view is that biological research, clinical research, and healthcare are at their best when coupled with the most accurate, highest throughput and innovative technology and analysis. He uses this view to motivate the use of innovation to reduce the time between data generation and data interpretation and has taken this philosophy into the role of Program Manager for Galaxy Australia, to run and help promote this important Australian resource to all life science researchers. On behalf of the Galaxy Australia team Gareth was very proud to receive this year three Australian Information Industry Association Queensland iAwards; the Infrastructure and Platforms Innovation of the Year award, the Community Services Markets award and the Queensland Premier’s iAward for Public Sector Innovation.

Simon Gladman

 

Gareth Price