Success of BioCommons-ELIXIR partnership showcased on the international stage

A showcase of outcomes that are being realised through international collaboration between life science data infrastructures were recently discussed by the global research infrastructure community at an international gathering. 

The 2024 International Conference on Research Infrastructures (ICRI 2024) explored global trends, challenges, and opportunities in research infrastructure. The December meeting was held in Brisbane - the first time ICRI has been hosted in the Asia Pacific - and attracted policymakers, research institution leaders, facility operators, users and researchers. Around 420 people from 50 nations travelled to Australia, including delegates from 11 Southeast Asian and Pacific nations, for this year’s event. Another 500 people joined online from 39 nations. 

Significantly, the 2024 event was the first ICRI to focus on Indigenous knowledge and engagement. Organising the meeting was a joint effort between Australia’s national science agency (CSIRO), the European Commission, and the Australian Department of Education. 

With a Euro-Australian bioinformatics infrastructure collaboration agreement now into its fifth year, representatives from BioCommons and ELIXIR hosted an official side event, Euro-Australian research infrastructure collaboration in the molecular life sciences. Partners described fruitful outcomes for the global community, and key examples from BioCommons’ perspective were highlighted, including our enablement of:

• A  multi-week coworking session for Galaxy Australia and Galaxy Europe staff in Brisbane in 2023

• Shared product ownership of WorkflowHub between Australian and European colleagues

• Launch of Australia’s DReSA and incorporation of its codebase into ELIXIR’s TeSS

• The Australian Outpost of ELIXIR’s BioHackathon Europe in 2022, 23, and 24

• Codevelopment of genome assembly and annotation pipelines for biodiversity efforts

• Connection building to target efficient data publishing and re-use in a global context 

Presenters at this event included Kelly Scarlett from Bioplatforms Australia who set the context within the National Collaborative Research Infrastructure Strategy (NCRIS), Ondřej Hradil representing the European Strategy Forum on Research Infrastructures (ESFRI), Jeff Christiansen and Nigel Ward representing Australian BioCommons, Tim Hubbard representing ELIXIR, Fotis Psomopoulos representing CERTH and ELIXIR Greece, and Gerry Reilly representing BioFAIR UK.

To capture the international goodwill generated and the progress made during the ICRI conference, organisers published The Brisbane Statement. It encourages all research infrastructure (RI) stakeholders to actively consider the role of RIs in addressing global challenges, and how strengthening international RI collaborations can help solve them.

Australian BioCommons is supported by Bioplatforms Australia, which is enabled by NCRIS.

An international approach to harnessing AI opportunities in the life sciences

From left to right: Prof Ewan Birney, Andrew Gilbert, Dr Jeff Christiansen, Prof Andrew Lonie

Many of us are exploring the opportunities that AI brings to life sciences. Australian BioCommons and Bioplatforms Australia recently hosted Prof Ewan Birney, Deputy Director General of the European Molecular Biology Laboratory (EMBL) and Director of EMBL’s European Bioinformatics Institute (EMBL-EBI) at the University of Melbourne to share his views in a workshop: Exploring opportunities in Life Sciences AI. 

The workshop focused on existing activities in Australia and global AI developments, with a facilitated discussion on how to build effective collaborations between infrastructures and researchers in the AI-life sciences space, and what opportunities there are for Australia to collaborate more closely with the EU across life sciences infrastructure, data, informatics, training and research programs.

Prof Birney’s visit included a keynote address at the iconic Shine Dome in Canberra. Co-hosted by EMBL Australia and Bioplatforms Australia, the event included talks from international and Australian experts, and drew scientists and senior leadership from a range of organisations, including CSIRO, Monash University, UNSW, the Australian National University, the University of Canberra, the Australian Government Department of Education, NCRIS projects, Snow Medical and Research Australia, as well as postdoctoral researchers and students. Read more about Prof Birney’s presentation in EMBL Australia’s news item.

As well as helping BioCommons to coalesce its approach to facilitating AI application in life sciences, the visit has strengthened the connection between BioCommons and EMBL and has led to ongoing discussions about future cooperation. Meeting in person was an excellent opportunity to clarify our intersecting needs, and establish a foundation to work together more closely into the future.

Australian Outpost of BioHackathon Europe connects researchers to help shape global bioinformatics advances

A diverse collection of Australian researchers gathered in Brisbane for the latest edition of ELIXIR’s BioHackathon Europe. Thanks to the ongoing collaboration between Australian BioComons and ELIXIR, Australian life scientists had a powerful opportunity to shape global bioinformatics advancements, while networking with other life scientists both at home and abroad.

From 4 - 8 Nov, 18 keen Aussies worked from 12 - 9:30 pm each day to allow overlap with the European participants. This year our group worked across three projects:

One team developed a prototype data model converter that makes it easy to switch between data models for a given biomedical cohort. The team built mappings between common data formats OMOP and FHIR and central ‘meta cohort’ format, plus made a front end interface that enables data upload, selection of the data model, selection of the data format, and download of the converted dataset. This team was highly collaborative, with members from the BioCommons Human Genome Informatics team, software and bioinformatics engineers from Children’s Cancer Institute (CCI), bioinformaticians and data scientists from the Sydney Informatics Hub, and a University of Melbourne Masters of Genomics and Health student. 

A particularly diverse team with representatives from BioCommons, Melbourne Bioinformatics, Curtin University, University of Sydney (Threatened Species Initiative), University of Tasmania, Symbio Labs, and QUT contributed to the FAIRtracks metadata schema. Their wide range of experience across conservation, agriculture and biodiversity was a new angle for a project that had previously focused on human data. The Aussies built many new connections and had a strong influence on the extension of the FAIRtracks schema into the life sciences.

Another team worked on was a key component of a larger European effort to ensure the global Galaxy project is sustainable and resources remain clearly accessible. Building the ‘Galaxy Codex’ led to major improvements in the findability of Galaxy resources such as tools, workflows and training material across microbiology, single cell omics, and proteomics.

Outside of the project work, the local team spent plenty of time getting to know each other and building their professional relationships, plus ate plenty of Spanish food to feel more connected to the Barcelona event! Dr Tim White, Data Science Software Engineer at the Sydney Informatics Hub, found collaborating in real time invaluable:

Typically in software development we are presented with the final product and don’t get to see the drafting process. It was fantastic to collaborate with the CCI software engineers to develop the code together and share what we consider at each stage of development.

Meanwhile, Dr Christian Fares, Senior Software Engineer at CCI, said their team found significant benefit from working outside of their usual area:

Our day to day roles wouldn’t normally encompass data model conversion, so we gained fantastic experience in a new area. We’ve been intending to learn more about the FHIR data standard, so attending the Aussie Outpost was a great opportunity, and we’ll be sharing our learnings with the rest of the CCI team soon.

 We'll be bringing together another team for the next BioHackathon Europe in Nov 2025 - keep your eyes peeled for our call for applications mid next year! In the meantime, read ELIXIR’s summary of BioHackathon Europe 2024.

Supercomputing access powers development of a new multi-omics resource

A new bioinformatics platform to support multi omics has been released by Australian members of the International Cannabis Genomics Research Consortium (ICGRC). The web accessible platform is designed for data sharing, hosting and analysis and is freely available for the global cannabis research community to use. 

Researchers from Southern Cross University, Locedie Manseuto and Dr Ramil Mauleon wanted to build an authoritative, open-science focused, web portal that would support multi-omics research on Cannabis sativa. Leveraging their ongoing connection to Australian BioCommons via the multi-omics community, Loc and Mau sought support from the Australian BioCommons Leadership Share (ABLeS) to help build a key feature of the web portal: CannSeek. The CannSeek database contains approximately 100 million single-nucleotide polymorphisms (SNPs, pronounced ‘snips’). As part of his PhD thesis, Loc produced CannSeek with support from the Australian BioCommons Leadership Share (ABLeS):

We needed access to a large supercomputing allocation to allow us to analyse the entire collection of multi-sample Cannabis sativa next-generation sequencing data available in NCBI (over 2,500 samples in Dec 2022). Our allocation on NCI’s Gadi supercomputer via ABLeS was instrumental in analysing such a large quantity of sequence data.

Loc continued to work on Gadi to optimise a variant calling pipeline that combines both GATK and Parabricks software.

We deployed the optimised variant calling pipeline to compare three reference genomes with the 2,500 next-generation sequencing samples. We identified 90-100 million SNPs that form the CannSeek database. Compare this to the roughly 30 million SNPs from 3,000 rice samples and you can see why we needed the supercomputing resources!

Mau notes that the computational challenges didn’t end there:

The Gadi supercomputer was equally instrumental in solving our next challenge of finding a small (~1,500) subset of SNPs from the CannSeek database that would allow fingerprinting and differentiation of samples from the Cannabis sativa population. The small subset was critical to prepare, as it’s far too expensive to use ~30M SNPs for routine sample fingerprinting!

The ICGRC web portal contains several other omics tools like a JBrowse genome browser, a gene function database search, and an expression heatmap.

Learn more about the development of the ICGRC portal and the CannSeek database:

• Read: Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research

• Read: CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa

• Watch: Loc’s presentation at the Gigascience Press Seminar Series. 

Learn more about ABLeS on our website, or watch a 10 minute overview of the service. 

First batch of clinical data arrives in new data platform

A large collaborative effort striving to take the next leap toward protecting Australians at risk of coronary artery disease recently made significant progress. The first batch of clinical data for the Australian Cardiovascular disease Data Commons (ACDC) has arrived and is now loaded onto the project’s secure staging environment.

The dataset is from the Baker Heart and Diabetes Institute’s Australian Diabetes, Obesity and Lifestyle Study (AusDiab), a national population-based survey of 11,247 adults which is examining the natural history of diabetes, pre-diabetes, heart disease and kidney disease among Australian participants. AusDiab began in 1999 and is still following up with participants - making it Australia's largest longitudinal study in the field.

The ACDC project has drawn together an amazing array of clinicians, researchers, digital infrastructure experts, and consumer representatives. Work on the platform is ongoing, with data modelling, testing and validation continuing with partners from Baker Heart and Diabetes Institute, ACvA, The University of Sydney, 23Strands, CSL Limited and 18 cohort custodians. In the years to come, the platform will improve the capacity for Australian medical researchers to undertake discovery and translational research, specifically cardiovascular risk assessment and treatment.

Australian BioCommons is leading the implementation of the digital infrastructure underpinning ACDC, using the Gen3 data commons platform. Ultimately, the ACDC will become a critical data infrastructure housing pooled data from approximately 400,000 individuals representing up to 18 clinical cohorts from across Australia. 

Learn more about how we are building the ACDC.

Australian meeting strengthens international ties in human genomics

Australian BioCommons recently brought together a global group of research infrastructure specialists working at the forefront of genomics data sharing and management. Seizing the rare opportunity to meet face-to-face created by the GA4GH Plenary held in Melbourne, members gathered to explore shared challenges, common interests and opportunities to deepen ties for mutual benefit.

The organisations and projects represented included:

• Australian BioCommons

• Australian Genomics

• BROAD Institute

• Canadian Distributed Infrastructure for Genomics (CanDIG)

• ELIXIR

• EMBL's European Bioinformatics Institute (EMBL-EBI)

• European Genomic Data Infrastructure (GDI)

• Global Alliance for Genomics and Health (GA4GH)

• IT Centre for Science, Finland (CSC)

• McGill University

• Murdoch Children’s Research Institute (MCRI)

• National Computational Infrastructure (NCI)

• Ontario Institute for Cancer Research (OICR)

• University Health Network

• University of Melbourne Centre for Cancer Research (UMCCR)

The two day meeting opened with presentations detailing the genomics landscapes in Europe, Canada and Australia, showcasing the tools and techniques deployed by each organisation. These presentations uncovered significant convergence on technology solutions across the globe. Dr Mallory Freeberg, Human Genomics Team Lead at EMBl-EBI, noted that:

The chance to meet in person made it abundantly clear that challenges faced in human genomics are shared worldwide, and that we can learn so much from each other through our collaborations. The meeting significantly strengthened our existing relationships, and I look forward to continuing to grow our global human genomics community.

The Australian BioCommons Human Genome Informatics team relished the chance to dive into the finer details. Discussions around common technology solutions, such as GA4GH’s Beacon for handling data discovery, and using metadata standards like HPO and OMOP, were a clear standout that the team will apply to their ongoing work. Dr Conrad Leonard, Technical Lead of the Human Genome Informatics team, said:

I’m very excited for the potential of future collaborations. The opportunity to partner with the worlds’ leading scientists and technologists in this space is invaluable in our efforts to deliver genomic data sharing solutions for Australian researchers.

Overall, the meeting strengthened connections between Australian, European, and North American human genome informatics organisations, and set the stage for potential future partnerships that will drive research progress through provision of critical research infrastructure.

Read more about Australian BioCommons’ human genome informatics activities.

New high-capacity multi-omics platform attracts MRFF Critical Infrastructure funding

Australian BioCommons is part of a powerful new collaboration to build critical national research infrastructure that addresses unmet needs through new discovery and diagnostic capability in multi-omics. $15.83M of combined funding will support creation of the OMIX3 Platform, which will deliver integrated proteomics, lipidomics and metabolomics analysis of biological samples. 

Significant co-investment from partners including Bioplatforms Australia, Thermo Fisher Scientific and the University of Melbourne was complemented with funding from the Australian Government’s Medical Research Future Fund’s Critical Research Infrastructure initiative. The development of this world-leading multi-omics platform will expand existing NCRIS-funded infrastructure and leverage an outstanding collaborative network of researchers, clinicians and commercial partners.

The OMIX3 Platform will be an integrated high-throughput, multi-omics facility for processing clinical samples, from point of collection and biobanking, through to comprehensive, proteomic, metabolomic and lipidomic analysis on parallel mass spectrometry platforms. Australian BioCommons’ Human Genome Informatics team will contribute their extensive experience in developing sensitive data storage, sharing and analytics capabilities.

Led by the University of Melbourne’s Professor Olivia Carter, the OMIX3: High-capacity integrated multi-omics project includes partners and collaborators from Melbourne School of Psychological Sciences, Murdoch Children’s Research Institute, Melbourne School of Biomedical Sciences, Melbourne Dental School, Thermo Fisher Scientific, Australian BioCommons and Bioplatforms Australia.

You can learn more about the project by reading these announcements from other partners:

• MRFF funding for Australia-first research infrastructure project (Melbourne School of Psychological Sciences, the University of Melbourne)

• Researchers awarded $36m funding from MRFF for projects across health and science (the University of Melbourne)

Community-led design helps create Galaxy Australia’s Proteomics Lab

Galaxy Australia’s Proteomics Lab interface.

The new Galaxy Australia Proteomics Lab is now offering a customised, user-friendly view of Galaxy Australia that provides rapid access to a range of sophisticated proteomics resources alongside the compute proteomics researchers need.

Analysing proteomics data within Proteomics Lab is a smooth experience, with common tools conveniently sorted into categories. Each tool comes with descriptions and examples of required inputs, and includes links to tutorials and support. There’s also pre-organised test data available for key tools, making it faster to get started!

The Australian Proteomics Bioinformatics Community championed the development of Galaxy Australia’s Proteomics Lab, sharing their needs in quarterly meetings, including an in-person community forum held earlier this year. Assoc Prof Matt Padula, Director of the Lipidomics and Metabolomics Core Facility within the School of Life Sciences and Proteomics at University of Technology Sydney, and proteomics community member, found the community-led design approach particularly valuable:

It’s helped us realise the breadth of requirements from researchers with varying levels of proteomics knowledge. This field's complexity has led to misunderstandings about its capabilities and how to analyse data effectively. We’ve been able to design Proteomics Lab to assist researchers analyse proteomics data appropriately, with rapid access to guidance.

Matt expects Proteomics Lab will particularly benefit researchers who are beginning their proteomics journey:

The Lab will be an efficient training tool for both researchers and coursework students learning proteomics. It provides a lower barrier to entry, and the interfaces are streamlined compared to those of the desktop versions of the software, hiding complicated and potentially unnecessary settings that should often be left alone.

Proteomics Lab pairs perfectly with the computing power of Galaxy Australia, which is underpinned by computational resources provided by AARNet, ARDC Nectar Research Cloud, the University of Melbourne, QCIF, Pawsey Supercomputing Research Centre, National Computational Infrastructure, and Microsoft Azure. Access to this fully-subsidised compute via the Galaxy Australia Proteomics Lab is expected to improve efficiency for researchers using proteomics services like those accessing Matt’s Facility:

Now researchers at my Facility won’t have to wait for desktop computers to become free, and facility staff won’t have to manage access, freeing up everyone’s time.

Proteomics Lab is the latest release in a series of Labs that support different research domains. If you are an Australian researcher with an interest in proteomics, be sure to try out the new Galaxy Australia Proteomics Lab now!

The Australian Nextflow Seqera Service: Your one-stop shop for Nextflow workflows

A new service provides access to a centralised command post for Australian researchers to manage, launch and monitor their Nextflow workflows. This subsidised access to Seqera Platform is now available through a licensing agreement between Seqera and Australian BioCommons.

Researchers can run workflows on the Australian Nextflow Seqera Service using their existing allocations at their preferred compute infrastructure, including local high-performance computers (HPCs) or commercial cloud services. Alternatively, national compute resources at Tier 1 facilities are available through the complementary Australian BioCommons Leadership Share (ABLeS). Dr Magdalena Antczak, Bioinformatician at QCIF, found this connection particularly helpful:

Thanks to the resources allocated to us by the ABLeS program, we were able to launch the ONTViSc pipeline detecting viruses from plants from within the Australian Nextflow Seqera Service. We could test the pipeline thoroughly using multiple high-performance computing infrastructures and cater for users without easy access to bioinformatics services.

Out-of-the-box configurations for running Nextflow pipelines on Pawsey Supercomputing Research Centre’s Setonix and National Computational Infrastructure’s (NCI’s) Gadi are available. Or if research groups need a more bespoke approach, extensive technical documentation and the friendly user guide will help tailor the Australian Nextflow Seqera Service to their needs.

Dr Julie Iskander, Lead Research Computing Engineer at WEHI, has seen the benefits for researchers first hand:

WEHI’s Research Computing Platform Engineering team supports WEHI researchers through software engineering services to build tools and pipelines. Seqera Platform has helped us a lot. We've been able to invite our researchers to jump in and see if the platform meets their needs. With the support of the BioCommons, we've had 15 researchers across 7 of our different research groups try it out. It's made launching pipelines easy for researchers who are not familiar with linux systems and command line. This helps them to independently run complex workflows on the HPC, with minimum knowledge of its underlying complexities.

WEHI was one of the 33 groups across 16 Australian research institutes taking part in BioCommons’ successful two-year pilot program, supported by Pawsey, NCI, Sydney Informatics Hub, Queensland Cyber Infrastructure Foundation (QCIF) and the University of Melbourne. Over that time, Seqera worked with BioCommons to understand how to best support the local Nextflow community and match Australian researchers’ sophisticated usage of the workflow management and data analysis environment, Seqera Platform.

The Australian Nextflow Seqera Service is fully subsidised for groups of up to three users to work collaboratively in a dedicated workspace. Larger organisations can explore the service at no cost by bringing an unlimited number of users to their dedicated workspaces for their first year of use (annual fee applies thereafter).

The Australian Nextflow Seqera Service is a key component of BioCommons’ vision to build an ecosystem of data analysis infrastructures that empower breakthrough discoveries.

Find out more about the Australian Nextflow Seqera Service and register to get started today!

The Australian Nextflow Seqera Service is operated by Australian BioCommons in collaboration with Pawsey, NCI, and Seqera. It is hosted on Amazon Web Services and supported by Bioplatforms Australia via NCRIS funding.

Attend AMSI’s BioInfoSummer with support from Australian BioCommons

Australian BioCommons is once again supporting undergraduate and postgraduate students from around the country to travel to AMSI BioInfoSummer in Melbourne. 

Australian Mathematical Sciences Institute’s annual event brings together people from all disciplines to discuss the latest research and developments in bioinformatics. This flagship conference is well known for connecting those new to bioinformatics research with leading experts, and enabling cross-disciplinary networking under a shared interest in bioinformatics.

AMSI BioInfoSummer is being held at the University of Melbourne with three themes: whole-cell modelling, machine learning and AI for genomics, and emerging technologies. The emerging technologies theme includes a two-part workshop ‘Hello Nextflow!’ presented by Australian BioCommons and our Sydney Informatics Hub Node at the University of Sydney. 

Previous attendees have described BioInfoSummer as “action-packed lectures and hands-on workshops from the best in the bioinformatics field, from Australia and abroad.”

If you’re an undergraduate or postgraduate student who could benefit from full or partial travel and accommodation funding to participate in the December conference, apply before 14 October!