Ready-made training environments for uplifting computational science skills in plant biosecurity

Molecular biologists and plant pathologists recently came together to learn how to use Galaxy Australia to implement small RNA sequencing (sRNA-Seq) for the detection of viruses and viroids in imported plants at the Post Entry Quarantine (PEQ) Facility in Mickleham, Victoria.

The Science and Surveillance Group from the Australian Government’s Department of Agriculture, Water and the Environment took part in a three-day viral pathogen detection workshop from 23-25th May. During the intensive hands-on training, the group of fourteen learnt how to process sRNA-Seq data using a bespoke Galaxy Australia pipeline, GA-VirReport.

Participants made the most of Galaxy Australia’s tools and dedicated job queue for training during the workshop. Instructors from the Queensland University of Technology (QUT) reported that the workshop received a unanimous 5-star rating from attendees. The feedback received from the mostly beginner audience was that almost everyone left feeling ‘very comfortable’ performing basic functions in Galaxy Australia, as well as using the tailored Galaxy Australia workflows for processing sRNA-Seq data and reporting positive detections.

Researchers are increasingly using Galaxy Australia for their training events as it provides a stable service for the planning and delivery of training. Supported by ample computing resources to scale with the size of the event, it comes with a robust set of over 1,500 tools and offers a dashboard of attendee progress that facilitates real-time management of jobs and immediate troubleshooting - vital both in face-to-face and online training events.

In addition to the pathogen detection workshop, over 4,500 participants taking part in 42 other training events have logged on and run their hands-on exercises on Galaxy Australia in the past 18 months. These include training delivered by individual universities, national consortia, international conference workshops and global training events - including the wildly successful Galaxy Training Network Smorgasbord.  

Dr Ruvini Lelwala, Research Associate in Bioinformatics at the School of Biology & Environmental Science, QUT, was one of the instructors in the hands-on training in processing sRNA-Seq data for virus and viroid testing in plants. Dr Lelwala is an experienced user who leverages the Galaxy Australia service to develop  enhanced diagnostics for the detection of exotic plant pathogens.

“I would like to thank the Galaxy Australia support team for their continuous support throughout the project which extends far beyond this workshop. The workshop itself was successful in delivering bioinformatics training to molecular biologists with limited experience in handling high throughput sequencing data using the Galaxy Australia platform.”

High Throughput Sequencing enables the rapid detection of viruses and viroids in imported plant material in a single test and can accelerate the release of quarantined plant genetic stocks. This research ultimately aims to give growers faster access to new plant stock and a competitive boost to the Australian horticulture sector.   

All Australian scientists can utilise the simple training interface and sophisticated behind-the-scenes infrastructure to support their training events. For further information about how Galaxy Australia can support your training events, contact the Galaxy Australia team at help@genome.edu.au.

The two projects underpinning the GA-VirReport workshop are: 

The project Improving access to new germplasm through faster and more accurate diagnostics (MT18005) is funded by Hort Innovation using citrus, nursery, raspberry and blackberry, fresh and processing potato and table grape research and development levies, co-investment from Queensland University of Technology and contributions from the Australian Government. Hort Innovation is the grower-owned, not-for-profit research and development corporation for Australian horticulture. 

The project Transformation of exotic plant disease testing at PEQ, Mickleham by implementation of high-throughput sequencing (BIP202048) is funded by the Department of Agriculture, Water and the Environment (DAWE) Biosecurity Innovation Program.