Wrapping up the ‘Bring Your Own Data’ project and a look to the future
Important Outputs
- Australian Apollo Service
- Australian Alphafold Service
- Australian Fgenesh++ Service
- Grew Galaxy Australia significantly, from two to seven million submitted jobs
- Established Galaxy Australia’s TIaaS and the Genome Lab
- Tool Finder
- Seqera Platform pilot
- Bioimage, a purpose built bioinformatics environment on the command-line
Four new national services, major expansions to Galaxy Australia, 15 training workshops and webinars, many specialised workflows, and even more stories of impact, all thanks to collaborative efforts of 12 organisations. It’s fair to say that the Australian BioCommons ‘Bring Your Own Data’ (BYOD) project met its aim to enable highly accessible, available, and scalable data analysis and sharing capabilities for the benefit of Australian life science researchers.
Winding down at the end of 2023, the BYOD Expansion project’s legacy will continue through the delivery and constant improvement of our national services.
The project began in June 2019 thanks to investment from BioPlatforms Australia and the Australian Research Data Commons (ARDC), and brought together a large group of collaborators and co-investors including AAF, AARNet, Melbourne Bioinformatics, NCI, Pawsey, QCIF via the Queensland Government RICF fund, The University of Sydney, AGRF, Griffith University and Monash University. There were three focus areas: web-based bioinformatics workbenches for life sciences researchers, a complementary command line interface (CLI)-focused platform, and creation of data infrastructure connecting ‘omics instruments and reference datasets to the analysis infrastructure. Work in these areas has had a wide ranging and extremely positive impact on the life sciences research landscape, as showcased in the words of infrastructure end users.
TESTIMONIALS
Tool Finder will be a really useful resource for researchers, particularly those who are just getting started and want to understand what software is available for their analysis and what computing platform would be most suitable. It’s awesome to have all of that information on hand in the one place!
Dr Parice Brandies, The University of Sydney
Galaxy Australia is intuitive to use, it’s easy because students don’t have to install software, it has lots of really good documentation and visualisation, and all of this helps the students to understand what they are doing and more importantly why they are doing it.
Dr Kylie Munyard, Curtin Medical School
The Fgenesh++ service has helped us easily and efficiently annotate multiple diverse genomes to a high standard.
Dr Kate Farquharson, The University of Sydney
For my PhD project I assembled close to 4000 RNA-Seq datasets from samples from all over the world - a task that would have been impossible without Galaxy Australia.
Dr Rhys Parry, University of Queensland
So much software gets left without regular updates and from year to year you realise that it isn’t maintained or updated. So we look for things that are stable - this is the reason we call on the Australian Apollo Service.
Assoc Prof Charles Robin, University of Melbourne
We are looking at how a particular genus of plant viruses evolved to only infect plants. We make virus-like particles in order to determine the structure of viruses and also for drug discovery and biomedical use. AlphaFold was used to check for evidence of a core structural domain of a putative coat protein and the fact that it was there gave us the confidence to go on and make virus-like particles.
Dr Frank Sainsbury, Griffith Institute for Drug Discovery
TIaaS helps keep workshops on track. Trainers have live insight into how participants’ jobs are running and can identify sticking points almost before they happen. The special training queue means that everyone has a consistent experience. Even large jobs submitted simultaneously from all around Australia run fast.
Dr Melissa Burke, Australian BioCommons
The Bioimage was a great place to enter the world of bioinformatics and really helped me to upskill on the command-line. I was able to jump right in and make use of Nextflow pipelines, Singularity containers and interactive Rstudio sessions.
Alexandra Boyling, ANZAC Research Institute
Looking ahead, BioCommons are establishing two new activities - the ‘Methods Commons’ and ‘BioCLI’ to continue where BYOD has left off. Stay tuned for more in this space!
The Australian BioCommons BYOD Expansion Project is funded through NCRIS investments from Bioplatforms Australia and the Australian Research Data Commons (http://doi.org/10.47486/PL105) that are matched with co-investments from AARNet, Melbourne Bioinformatics, NCI, Pawsey, QCIF via the Queensland Government RICF fund, The University of Sydney, AGRF, Griffith University and Monash University.