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 ‘Workflow Commons’ and ‘BioCLI’ to continue where BYOD has left off. Stay tuned for more in this space!

Read a full summary of the BYOD Expansion project

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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.

Australian satellite of BioHackathon Europe 2023 underscores the universal language of scientific collaboration

The Outpost team consisted of Cameron Hyde (QCIF, University of the Sunshine Coast), Igor Makunin (QCIF, University of Queensland / Australian BioCommons), Anna Syme (Melbourne Bioinformatics / Australian BioCommons), Michael Charleston (University of Tasmania), Locedie Mansueto (Southern Cross University), Johan Gustafsson (Australian BioCommons), Mike Thang (QCIF, University of Queensland / Australian BioCommons), Tom Harrop (Melbourne Bioinformatics / Australian BioCommons), and Siyuan Wang (Symbio Laboratories).

To bridge the geographical gap, an Australian team participated in an innovative collaboration to once again join BioHackathon Europe remotely. Providing a powerful opportunity for Australian contributors to shape global bioinformatics advancements, this fun annual ELIXIR Europe - Australian Outpost also offers a welcoming platform for networking with local and international peers.  

From 30 Oct to 3 Nov, a diverse team from around Australia converged on a Brisbane hotel, turning the apartment into a hub of innovative coding challenges. Ten people worked 2:30 pm - 12:30 am each day, while connecting live with the rest of the teams in Barcelona and online. The highly anticipated annual event saw 350 participants from around the world come together to work on 35 projects. 

Reflecting the rich multicultural fabric of Australia and the global nature of the event, the team showcased a remarkable diversity of backgrounds. Composed of individuals born in England, China, the Soviet Union, the Philippines, Malaysia, New Zealand, and Australia, and ranging from postgraduate students to seasoned professors, our team brought together a tapestry of experiences, perspectives, and expertise.  We welcomed familiar faces and newcomers who responded to our public call for interest, and participants from both academia and industry. They brought interests in mathematics, biology, computing and bioinformatics and exchanged more than a few skills along the way.

Our group mirrored the inclusive spirit of the BioHackathon, working hard into the night to contribute to one or two of our chosen projects:

• Galaxy ENA Upload as an Interactive Tool

  A big leap forward was made to the process to interactively build the metadata required for successful ENA data submission. This team worked on a new interactive Galaxy tool that allows a researcher to pick and populate one of 30+ ENA templates, and re-focused the ENA upload tool in Galaxy to accept only prepared ENA templates.

• Genome annotation and other post-assembly workflows for the tree of life

  This team contributed to a broad examination of analysis pipelines by running annotations for several species using multiple Galaxy tools. The results have kicked off ongoing work to consolidate tools and relevant settings into user-friendly workflows.

• Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific Communities

  The project created an interactive table prototype that increases the findability of the Galaxy microbiome analysis tools, and which can now be reused by other Galaxy domain communities. The process of updating bio.tools registry entries and linking each Galaxy tool to these entries was started, and will ensure the completeness of the table metadata over time.

Aside from the progress made on each of the projects, the Outpost provided the opportunity to “meet new people and continue building working relationships with international colleagues” which has already resulted in “multiple collaborative outcomes from the projects” according to Dr Johan Gustafsson, BioCommons’ Bioinformatics Engagement Officer. Siyuan Wang, from Symbio Laboratories, said: “The Outpost was a perfect opportunity to meet new people in a similar field and I got to work on exciting projects that I wouldn’t normally have had a chance to do.” From the European side, Dr Nicola Soranzo, who currently works at the Earlham Institute as Galaxy Platform Development Officer found the virtual connection worked very well, and was thankful for a “great collaboration with the Aussie Outpost!”

ELIXIR generously supported the in-person attendance of Dr Gareth Price from QCIF. As Galaxy Australia’s Lead, Gareth was well placed to act as our Barecelona connection point. He helped to raise awareness of our Outpost and facilitate discussions and presentations on behalf of the Aussies. We are extremely grateful to ELIXIR for working with us in the lead up to the event to make sure our contributions were optimised.

We’ll bring together a new team for the next BioHackathon Europe in Nov 2024 - maybe you will join us next time!

New online tutorials embed genomics into conservation management decisions

Photo credits: Left Kate Quigley, centre Nick Bradsworth, right Carolyn Hogg.

A new online course is available that promises to increase the use of genetic data in Australian conservation management actions. Developed by the Threatened Species Initiative (TSI) and the University of Sydney in collaboration with some of Australia’s leading conservation geneticists, the tutorials have been made freely available to everyone via the Australian BioCommons YouTube Channel.

Genetics and genomics are powerful tools for understanding global biodiversity, with a wide range of applications for policy, ecology, translocations, evolutionary biology and more. The Conservation Genomics for Threatened Species Management course was developed by TSI, which brings a network of researchers into direct contact with conservation agencies and policy makers, enabling research outcomes to directly influence on the ground conservation decisions. As one of Bioplatforms Australia’s key Framework Initiatives, TSI reached out to BioCommons for support to edit and host their community’s content.  Prof Carolyn Hogg, Senior Research Manager, Australasian Wildlife Genomics Group at the University of Sydney, and Science Lead and Chair of TSI, brought together a panel of field experts to explain how cutting-edge genomics technologies, genetic tools and advanced computational biology can assist and guide conservation management strategies.

The inaugural @ThreatenedSpGen workshop on using genetics for conservation management was a hit! A great group of people from all over, really engaged in upskilling their genetic literacy. #ictc23 @ellemclennan @persoonia @BioplatformsAus @Sydney_Science @Science_DBCA pic.twitter.com/zumixBBW1p

— Prof Carolyn Hogg (@HoggCarolyn) November 12, 2023

The ten modules can be viewed independently, and the course materials have already been used at a workshop during the 2023 International Conservation Translocation Conference. The suite of videos will be added to over time, but so far feature speakers from the University of Sydney, Monash University, University of Adelaide, Australian National University, Minderoo Foundation, Arthur Rylah Institute for Environmental Research, Research Centre for Ecosystem Resilience at the Botanic Gardens Sydney, Taronga Conservation Society Australia, NSW Government Savings our Species program, and the Government of Western Australia Department of Environment and Conservation. 

You can learn more from Carolyn about how TSI is bridging the gap between genomicists, bioinformaticians, conservation experts and decision makers to help save Australian species by visiting the refreshed TSI website. Or watch her BioCommons webinar ‘Conservation genomics in the Age of Extinction’, to learn more about using cutting-edge genomics technology and advanced computational biology to assist in conservation management for species recovery.

View the Conservation Genomics for Threatened Species Management playlist

User experience insights help design better services for researchers

A key question is right there in the URL usegalaxy.org.au: How do you use Galaxy Australia? Australian BioCommons User Experience Designer, Mok, recently analysed the journeys that users take when accessing the Galaxy Australia service. Mok’s research has provided a clear direction for improvement that has been taken up by the international Galaxy project. Simple, fundamental changes are planned based on how you use Galaxy.

The Galaxy Australia team’s commitment to constantly improving the service required insight into the many different ways that researchers use Galaxy. Mok worked with Galaxy Australia’s user experience designer, Madeline Bassetti to examine the experiences of Australian users.

Mok’s findings provide a visual story of how researchers interact with Galaxy Australia, including developing personas for different types of users including bioinformaticians, e-research analysts and PhD students. Each persona has distinct characteristics (eg. their familiarity with using Galaxy), allowing the Galaxy team to further analyse user experience within the appropriate context and prioritise which new features and improvements to implement first.

Interactions with Galaxy Australia were investigated according to the stages of plan, collect, process, analyse, preserve, share and reuse, as described in the ELIXIR RDMkit data lifecycle.  Many users begin their journey at the analysis stage, however Mok’s research identified that Galaxy Australia has an important role to play at each lifecycle stage. By documenting users’ pain points, Mok identified opportunities and recommendations to improve Galaxy Australia across the whole data lifecycle. After a recent presentation at the Galaxy Community Conference, the international gathering of Galaxy developers shared that they “found the talk super helpful, particularly the user journey maps,” and noted that “this work is a huge time saver for the rest of the [international] Galaxy project.”

As a result, Mok was invited to present a full report at one of the Galaxy Community Calls, where US, EU and Australian Galaxy development teams gather to share updates and discuss improvements to the Galaxy. An international team has formed to combine Mok’s work with website analytics to gain further insights. Ultimately, this user journey research will inform future improvements to the entire Galaxy ecosystem.

Go ahead and look at the latest updates, start your own journey to use Galaxy, or if you have a deeper interest, consider joining a Galaxy Community Call in the future - everyone is welcome!

Bringing Seqera Platform to Australian researchers

Dr Steven Manos, BioCommons’ A/Director of the BioCloud, recently returned from Barcelona where he opened the global Nextflow Summit by presenting “The national Nextflow Tower service for Australian researchers.” He was invited to share his experience in recognition of the sophisticated Australian usage of the workflow management and data analysis space, Seqera Platform. 

A partnership involving Seqera Labs, Pawsey and NCI has allowed BioCommons to investigate how to best support researchers in their Nextflow workflow use across high-performance computing (HPC) and commercial cloud environments. Since July 2022, the Seqera Platform has been integrated with the Pawsey and NCI supercomputers as well as compute environments at WEHI, AGRF and AWS. The service is in use by 60 individuals from 20 research groups/organisations.

Once fully operational, the Australian Nextflow Seqera Service will offer a fully subsidised, centralised command post for Australian researchers to manage and run their Nextflow workflows. Users can bring their own supercomputing allocations, local HPC or commercial cloud services. Alternatively, access to compute can be provided through the Australian BioCommons Leadership Share (ABLeS). BioCommons is now inviting Australian life sciences research groups and organisations to express interest in joining the pilot project that is building this national service. For now, the call out is for experienced users/groups with access to compute infrastructure, Nextflow workflows and testing datasets ready for use, and the requisite expertise to manage their environment.

Did you know? Nextflow Tower has recently been rebranded “Seqera Platform”

A progress update on the Seqera Platform pilot project will be presented at the 2023 ABACBS Conference by Dr Ziad Al Bkhetan, Bioinformatics Application Specialist in the ABLeS program and Seqera Platform Service Lead.  As silver sponsors, we extend our long history of supporting the conference and we hope you will catch up with Ziad and other BioCommons staff to discuss the latest developments in Seqera Platform and other BioCommons services. 

Learn more about Seqera Platform via this Australian BioCommons webinar.

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The Seqera Platform pilot project is delivered through the Australian BioCommons ‘Bring Your Own Data’ Expansion Project. The 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.

BioCommons strengthens connections with the Asia-Pacific region

BioCommons has strengthened connections with the Asia-Pacific region at the 22nd International Conference on Bioinformatics (InCOB) hosted by the Asia-Pacific Bioinformatics Network (APBioNet) in Brisbane. In line with our mission to uplift life sciences digital research, BioCommons training capabilities and services were on show at the conference. 

BioCommons provided virtual machines to support the Tyagi Lab at RMIT University and COMBINE to deliver an ‘Introduction to Machine Learning for Bioinformatics’ workshop on predictive modelling for genomics data for conference attendees. Attended by 25 people, this workshop is amplifying machine learning skills in the region and beyond. Find out more about how we enable events related to bioinformatics that benefit a national audience.

Dr Melissa Burke, BioCommons bioinformatics training specialist, attended a special session on bioinformatics education to hear how organisations and individuals are navigating the evolving landscape of bioinformatics education in the 21st century. 

Dr Gareth Price, Project Lead of the Galaxy Australia service, presented a talk on ‘Making bioinformatics more user-friendly with custom interfaces’ and the Galaxy Australia team developed new training materials to support wrapping of tools for Galaxy.

In 2024, bioinformatics societies of the Asia-Pacific region will unite at the first Asia and Pacific Bioinformatics Joint Conference in Okinawa, Japan around the theme of ‘Creating bioinformatics synergy across the Asia Pacific region.’ Find out more about the conference.

New framework to improve effectiveness and inclusivity of life science training

A first-of-its-kind framework termed the ‘Bicycle Principles’ advocates for actions that will improve the effectiveness and inclusiveness of professional development in the life sciences and beyond. 

Nearly all researchers participate in workshops or short courses to enhance their skill sets. However, there are almost no standards to guarantee training quality, and peer-reviewed evidence suggests that much of what is available is ineffective. 

The Bicycle Principles, developed through an international project led by Jason Williams (Cold Spring Harbor Laboratory) and Rochelle Tractenberg (Georgetown University) with support from the National Science Foundation (USA), provide a set of 14 recommendations to systematically strengthen short format training. The Principles represent the consensus amongst international experts on instruction in the life sciences including the BioCommons’ Christina Hall (Associate Director of Training and Communications) and Melissa Burke (Training and Communications Officer). They provide a framework through which instructors, programs, organisations and funders can prioritise evidence-based teaching, inclusiveness and equity as well as the ability to scale, share, and sustain training.

For researchers, the implementation of this framework could provide assurances of training quality, assisting them in maximising their professional skills, achieving career goals, and increasing the impact of their scientific work.

The Bicycle Principles framework is published in PLOS ONE and is accompanied by an implementation roadmap that demonstrates how individuals, groups, communities of practice and organisations can put the principles into action. 
Read more about the Bicycle Principles on the project’s website.

Funding boost to bring game-changing growth to BioCommons

Australian BioCommons is poised to undertake a period of significant growth following the Department of Education’s announcement of crucial new funding to Australia’s National Collaborative Research Infrastructure Strategy (NCRIS). This will deliver a variety of game-changing national infrastructure developments to support omics-based life science research, with Bioplatforms Australia allocating funding to the BioCommons over the 2023-27 period in three growth areas:

• Integrated analysis platforms for omics research through the development of a ‘BioCloud’ - a unified set of ‘research context aware’ digital services tailored to meet the requirements of life sciences researchers to work with molecular biological data, using bioinformatics tools and workflows on a variety of infrastructures.

• Foundational infrastructure for accelerating biodiversity research and conservation (Australian Tree of Life (AToL) Data Laboratories) bringing together national ‘omics data with multidisciplinary data (environment, climate, trait) and connecting these to build a portfolio of transparent and repeatable analytical tools supporting deeply informed biodiversity and biosecurity management decisions.

• A translational human ‘omics data infrastructure program (GUARDIANS) to drive a step change to cutting-edge national digital research infrastructure and unlock Australia’s potential in human ‘omics research through the provision of secure, scalable, and integrated data and analytics platforms.

These three projects will be delivered in collaboration with the growing network of research consortia and delivery partners established by the BioCommons during its first phase. 

This exciting announcement builds on a 2023-28 extension to the BioCommons project that is already underway. Having delivered significant outcomes in the first 5-year term, the contractual agreements required for a further 5 years of continuity are currently being bedded down. This will ensure ongoing support for critical national services and community building activities.

Planning for the three growth areas is already underway and will intensify over the next six months. Discussions will broaden to include key partners soon, with a view to formalising initial projects and engagements in early 2024. Expect to see many exciting announcements, invitations to participate, and new opportunities to join BioCommons activities in the near future.

The outcomes of the NCRIS 2023 Funding Round are published on the Department of Education website.

The Australian BioCommons is supported by Bioplatforms Australia. Read their announcement: Bioplatforms Secures Crucial Funding from NCRIS Program to Propel Frontier Omics Technology.

Students investigate beetle genetic variation using new Apollo training instance

Teaching genetics is easier and more effective now that a powerful online tool is being made available to Australian researchers and trainers. Students can use a tailored training instance of the web-browser accessible system, Apollo, for real-time collaborative curation and editing of genome annotations.

This new feature of the Australian Apollo Service allows trainers to focus on teaching genome annotation curation, without being burdened by installation and maintenance of Apollo. All the hosting and system administration of customised Apollo instances is taken care of for service users. Life scientists and research consortia based in Australia can apply for an instance that is ready-made for training, and is up to date with the latest release of the software. 

Molecular evolution and population genetics researcher, Assoc Prof Charles Robin signed on to the Australian BioCommons’ Apollo service through a recommendation from a colleague at Melbourne Bioinformatics. After facilitating some Australian BioCommons online workshops, Charles now uses an Apollo training instance when teaching genetics to third year undergraduates at the University of Melbourne. Each student is provided with their own login where they can visualise DNA sequences, perform annotations and explore without overwriting each others’ work. Charles finds Apollo ideal for teaching:

“It’s great that the transcriptome maps really well to the genome. By playing within Apollo, students get to see the AC / GT rule and how this can be reinforced by the transcript. Things like alternate splicing are also easily visualised.”

Two adult beetles, one with a CRISPR deletion in the gene called cardinal that is involved in eye colour. The genetic modifications were performed in Charles’ lab.

The class answers research questions like ‘which of the genes in this region includes this particular mutation?’ or ‘how do you find the candidate gene in this region?’ using real world data from a beetle with a gene mutation. Charles deliberately chooses genomes that are ‘untidy’:

“You want a non-model genome to identify gaps and changes. Students can have an expectation that all annotations on a genome are true, and using Apollo allows them to see that this is not the case.”

Charles rates the reliability of the software as a key factor in why he uses Apollo for teaching genetics:

“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.”

Using Apollo to curate genome annotations

The Australian Apollo Service performs all system administration, build and deployment of the instance on behalf of users, with support provided through a help desk, user documentation and training events. The deployment of a full technology stack, long term hosting of data, maintenance updates and security are all covered, providing customised, local instances of the Apollo software for individual genome projects or training. 

Australian BioCommons are working with Apollo project principal investigator Prof Ian Holmes to understand researchers’ needs within Apollo, with an aim to provide improved annotation and visualisation features for genome annotation research.

Launch Apollo to learn more

Australian BioCommons delivers collaborative distributed infrastructure to enable life science research. BioCommons partner QCIF is offering the Apollo Portal service, and it is underpinned by computational resources provided by the Pawsey Supercomputing Research Centre. These efforts are supported by funding from Bioplatforms Australia (BPA) and Australian Research Data Commons (ARDC). BPA and ARDC are enabled by NCRIS.

Automated testing with Selenium assures robust systems

To the untrained eye, the latest release of the Galaxy software is a long and technical list of 208 enhancements and 145 fixes of known issues, inherent to the development of a sophisticated analysis platform. But step back from the detail, and we can see a significant advance in the maturity of this global service. The enhancements heavily feature tests of the system’s robustness – code that is tasked with benchmarking new infrastructure and monitoring its performance to ensure users are getting the most out of their time spent computing. 

Software Engineer, Dr Nuwan Goonasekera, has championed the use of Selenium to test new infrastructure and deployments for Galaxy Australia for several years now. This suite of tools enables automatic testing of applications. Galaxy Australia makes use of Selenium to monitor user health of the service, by checking the time taken to perform various common actions that users need. By constantly testing the system, the team can monitor a custom dashboard that alerts them to any potential issues the instant they begin.

End-to-end testing is not just good software engineering practice, it should also be part of a holistic plan to measure scalability and monitor service quality that users experience day-to-day.

Dr Nuwan Goonasekera
Melbourne Bioinformatics, Galaxy Australia

Galaxy Australia’s testing and ongoing monitoring drives the constant improvements that underpin a professional service. Their modelling of the use of Selenium has resulted in the tool now appearing in the procedures of other Galaxy servers around the world. It featured heavily in the new global release of Galaxy 23.1, with the list of enhancements made to the new version including many mentions of Selenium code. 

After witnessing the value of Galaxy Australia’s usage of Selenium at a recent meeting for BioCommons partners, QCIF Software Engineer, Brigette Gonch, was keen to investigate how the tool might assist in her work on the Bioplatforms Australia’s Data Portal. Galaxy Australia’s move to a new data centre is currently using Selenium to confirm improved performance, and ensure that any kinks are ironed out before users are granted access to the new resources in November.