Galaxy Australia celebrates 8 million jobs to open 2024
University of Sydney researcher, Jess Hawes, recently demonstrated that Galaxy Australia is the platform of choice for many researchers conducting bioinformatics analyses. The team behind the service have been eagerly awaiting submission of the key 8 millionth job and were thrilled when Galaxy-newcomer, Jess, lodged a suite of jobs to support her fascinating PhD project.
Jess is part of Dr Alyson Ashe’s research group within the School of Life and Environmental Studies at the University of Sydney and has rapidly become a sophisticated user of Galaxy Australia who processes up to 300 Gb of sequence data at a time.
Prior to starting my PhD, I had never done any bioinformatics and the prospect of jumping straight into command-line was intimidating. My supervisor suggested I try Galaxy Australia first. The setup was so quick, there were heaps of guides, templates and shared workflows that I could use to start from, and there’s a massive global community with lots of support and tips. It has been a really good introduction to bioinformatics!
Jess is working to understand the molecular basis for epigenetic inheritance, using model organism C. elegans to investigate how histone modifications and small RNAs interact in the context of epigenetic inheritance. Her workflow is completed end-to-end without leaving the Galaxy Australia site: from preparing sequencing files, pairing them, trimming off the adapters, aligning the reads to a reference genome and calling peaks. With large amounts of data to process at once, Jess requested extra storage:
It was so easy to ask for extra storage and I had a response within days. The email from the team saying that I’d be able to access 2 TB was such a relief! And for free!
Jess finds the Galaxy web interface very user-friendly:
I love that it saves a lot of the parameters and inputs that lead to the generation of different files. This means I can easily work out which inputs and which variables lead me down the right path. I also love that within Galaxy, if one of my samples fails at step 3 of 10 in the workflow, all the future steps that rely on that sample pause. This means I can go back, find the step that failed, troubleshoot and then re-run that one sample. There’s even a little toggle option that means after this step successfully runs, all the following steps will also resume. This means I am not stuck repeating every single step every time for all my datasets when only one step fails – saving both my time and computing time!
Overall, Jess has improved a wide range of skills through her experience using Galaxy Australia, describing it as:
A really good introduction to working in a command-line setting. If I needed to, I’d be more confident jumping into the back-end side of things. But so far I haven’t needed to because everything is ready to go!
Jess is one of more than 30,000 researchers who have used Galaxy Australia in their work. If you haven’t already, head to usegalaxy.org.au to get started today!