How do you deliver bioinformatics training efficiently and effectively in Australia? Here’s how.

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This week Melbourne Bioinformatics is leading the delivery of another national bioinformatics training event through its hosting of the Australian BioCommons/EMBL-ABR Hub activities.

This 2 day workshop is delivered using a hybrid model first trialled in 2017 and rolled out in 2018. There are 150 registrants attending at locations across Australia: Australian National University, University of Adelaide, James Cook University, University of New South Wales, University of Melbourne, Pawsey Supercomputing Centre (Perth), University of Queensland, Hudson Institute and Monash University.

At each location, attendees link up to expert lead trainers – online via Zoom – to hear presentations and undertake hands on tutorials, supported by EMBL-ABR trained facilitators in each room. Using simple tools like google docs, attendees form a mini learning community to help each other along the way.

Positive evaluation of the model of delivery from past events has now led to ongoing funding assurances to expand the program over the next four years.

National eResearch communities and our own international bioinformatics counterparts, who are also dealing with the ‘tyranny of distance’, have expressed interest in this mode of delivery. Training Program Co-ordinator for the Australian BioCommons/EMBL-ABR, our own Dr Christina Hall, will talk more about her work on this program at eResearch in Brisbane in October. A paper is in preparation also.

Workshop details (recordings of all presentations will be made available after the event at this link)

Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow

Large bioinformatics analysis workflows are fragile ecosystems of software tools, scripts and dependencies and can present a challenge to the reproducibility of data analyses. One solution is the use of the workflow management systems which can be seamlessly executed across different computing environments (laptop/desktop to High Performance Computing).

The two-part workshop will implement a common analytical pipeline in both Nextflow and Snakemake, exposing participants to the core concepts of importance to both workflow managers, while also providing a means to compare and contrast the two.

This workshop is intended for researchers who already use bioinformatics workflows in their research, but who do not yet have knowledge of Nextflow or Snakemake. To participate you must be familiar with the Linux command line and have experience with at least one scripting language. The workshop is free.

For Christina and all team members across the EMBL-ABR network, great work!