Welcome!

Update June 2024:
These tutorials were initially developed for the Antibiotic Resistant Pathogens Initiative
Galaxy-based tutorials have now been merged into the Galaxy Training Network
Please check there for the most up-to-date material, as this page is no longer maintained

ABRPI training materials

Antibiotic Resistant Pathogens Initiative

• This site contains tutorials for using the analysis components of the omics.data.edu.au platform to perform various bioinformatics tasks on bacterial “omics” data.

• Tools covered by these tutorials include:

  • those within the Microbial Genomics Virtual Lab (the mGVL), which can be accessed either through the hosted ABPRI-Galaxy service, or by setting up your own mGVL instance (see below) and accessing via the Unix command line.

  • those within the hosted ABPRI-PathwayTools service.

• Tutorials are listed under the tabs in the top panel (Genomics, Transcriptomics, Proteomics, Metabolomics).

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• If you wish to set up your own instance (version) of the mGVL, follow the instructions here.

  • Note: at the stage where you select options in the GVL Launcher window, go to Show advanced startup options and under Flavor select Microbial GVL with Tutorial Indices. In this mGVL instance, you can use both Galaxy and command line tools. If you wish to use the command line tools on a different computer (e.g. your local computer), you would need to make sure the required tools are installed (e.g. Canu, Circlator, Pilon, SPAdes, etc.).

• For additional tutorials about how to use the Genomics Virtual Lab and Galaxy, see https://www.gvl.org.au/learn/