ABRPI training materials

Antibiotic Resistant Pathogens Initiative

  • The Food and Health Flagship is an RDS-funded project to provide cloud-based data services and tools for Australian Life Science Researchers to combine, analyse and interpret genomic, transcriptomic, proteomic and metabolomic data. The data platform will incorporate the Bioplatforms Australia Antibiotic Resistant Pathogens Initiative (ABRPI).

  • This site contains tutorials for using the ABRPI Microbial Genomics Virtual Lab (the mGVL) to perform bioinformatics tasks on bacterial “omics” data, either on the Unix command line or using the Galaxy system.

  • Tutorials are listed under the tabs in the top panel and are being added progressively.

  • 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 more information about how to use the Microbial Genomics Virtual Lab and Galaxy, see http://www.genome.edu.au/

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