Strengthening ties with European research infrastructures at ELIXIR All Hands

Photo credit: Mikael Wallerstedt

A special seat at an international table was recently reserved for Australian BioCommons to share insights and address the challenges of building and sustaining distributed life science data infrastructure. The invitation to represent Australia’s activities at the 2024 ELIXIR All Hands provided the opportunity to reach more than 500 professionals from over 25 countries. Participants shared their successes and looked to collaboratively address ongoing challenges facing life science research infrastructures.

ELIXIR, as Europe’s life science research infrastructure, has a mission that is closely aligned with that of Australian BioCommons, and we have maintained a collaboration strategy since 2020. With ongoing face to face interactions a key component of the strategy, Australian BioCommons was well represented at the 2024 All Hands meeting with Dr Jeff Christiansen, Dr Tiff Nelson, and Dr Ziad Al Bkhetan all attending in Uppsala, Sweden.

The BioCommons team joined stimulating discussions that addressed key areas in ELIXIR’s scientific vision including cellular and molecular research; biodiversity, food security and pathogen; and human data and translational research. Among these discussions, Ziad presented the Australian Nextflow Seqera Service while Tiff shared our array of infrastructure supporting genomics research in Australia. Tiff was particularly excited by the emerging focus on biodiversity:

As European research data infrastructures’ focus turns to biodiversity, our experience working with Bioplatforms Australia Framework Initiatives like the Threatened Species Initiative and the Amphibian and Reptile Genome Initiative becomes so valuable. We’re looking forward to continued discussions with ELIXIR’s biodiversity community.

Jeff also found great value in making connections with other national infrastructure providers at All Hands 2024, including having the opportunity to also visit the Swedish Node of ELIXIR, National Bioinformatics Infrastructure Sweden (NBIS) at SciLifeLabs in Uppsala to connect on topics of mutual interest.

It was fantastic to renew existing connections and meet international partners like NBIS in person. One highlight was the crossover in our efforts to better support omics data management at a national level, and researchers’ omics data submissions to international repositories.

Read ELIXIR’s summary of the meeting

Galaxy Australia well represented at GCC2024

Last month, Galaxy Australia team members took the rare chance to work alongside over 150 other Galaxy developers in the same time zone at the 2024 Galaxy Community Conference (GCC). With 28 countries represented in Brno, Czech Republic, GCC was the perfect meeting place to celebrate Galaxy’s successes, discuss the latest developments, and work together to improve the Galaxy platform that enables accessible, reproducible, and transparent computational biological research.

Catherine Bromhead (Galaxy Australia Infrastructure Team Lead) presented the latest developments on the Total Perspective Vortex, a job scheduling tool originally developed by the Galaxy Australia team. With even further nuanced controls available, the Aussie Vortex is being adopted by Galaxy services around the globe. 

Gareth Price (Galaxy Australia Project Lead) represented Australian interests at the Directions Summit, co-launched a forum for Galaxy users to have input on the Galaxy Project’s roadmap, and delivered the Australian section of the prestigious ‘State of the Galaxy’ annual talk. In his talk, Gareth explained that:

The Galaxy Australia team maintains a strong community focus when we develop new offerings. We’re particularly proud of delivering on requests for specialised commercially licensed tools and custom workbenches like the Genome Lab.

After four days of presentations and training workshops, the two day Collaboration Festival saw participants work on solutions and enhancements in a way that is only possible when the global team comes together. For Gareth, adapting the Genome Lab code so that it can be repurposed for any other domain across the world was a particular highlight. 

Galaxy Labs are a fantastic entry point for Galaxy users, and the team are excited to make Galaxy Australia even more accessible for a wide range of domain specialists by developing new Galaxy Labs. Stay tuned for new releases soon!

Work on Galaxy Labs will continue as just one of many exciting projects at ELIXIR’s BioHackathon. If you’re interested in a unique opportunity to participate in this significant global event and network with your international peers while working intensively on practical bioinformatics challenges, consider joining the Australian Outpost!

Read the full GCC2024 meeting report at Galaxy News.
If you’d like to keep up with plans for GCC2025, subscribe to the BioCommons newsletter or Galaxy Announcements.

WorkflowHub and nf-core collaboration enhances workflow accessibility

This media release was prepared by ELIXIR-UK with assistance from BioCommons and is re-published here without modification.

WorkflowHub, a prominent registry for computational workflows, now automatically registers workflows developed by nf-core, a community-driven initiative focused on developing best-practice workflows. 

The marriage of these two resources will not only allow new workflows to be included automatically, but also updated versions of existing ones.

Additionally, during the import process, workflows are automatically annotated based on the metadata provided by the nf-core community in their native development repositories. This ensures that the workflows are visible, well-documented and easily understandable, following the principles of FAIR (Findable, Accessible, Interoperable, Reusable) data practices.

Contributions from the nf-core community are now streamlined and automated, freeing up valuable time and resources for both WorkflowHub and nf-core teams to focus on creating high-quality workflows without the added burden of managing findability and accessibility.

Developments in WorkflowHub are steered by the joint Product Owners Prof Carole Goble, ELIXIR-UK, Dr Frederick Coppens, ELIXIR-Belgium, and Dr Johan Gustafsson, Australian BioCommons. Recognising the increasing importance of Nextflow as a standard for defining bioinformatics workflows, the team engaged with nf-core to automatically ingest nf-core workflows to WorkflowHub.

About WorkflowHub

WorkflowHub is a leading registry for computational workflows, providing a platform for discovering, sharing, and using workflows across various scientific domains. It aims to enhance the accessibility and usability of computational workflows, promoting collaboration and innovation in the research community.

About nf-core

Nf-core is a community-driven initiative focused on developing best practice workflows using the Nextflow workflow management system. It provides a platform for collaborative development and sharing of high-quality workflows, fostering reproducibility and efficiency in computational research.

About ELIXIR-UK

ELIXIR-UK is part of the European ELIXIR infrastructure, which supports life science research and its translation to medicine, the environment, and society. By integrating national bioinformatics resources, ELIXIR-UK aims to provide a sustainable infrastructure for biological information, ensuring that data is effectively managed, analysed and shared across the scientific community.

The UK Node, as well as the Belgium Node of ELIXIR, endorse WorkflowHub as a Node Service. 

Further details reach out to us at contact@elixiruknode.org

About BioCommons

Australian BioCommons is a digital infrastructure capability enhancing Australian life sciences research. BioCommons links Australian researchers with the tools, platforms, and expertise they need to undertake world-class research into the molecular basis of life.

BioCommons facilitates links between the Australian research landscape and international platforms and communities, and contributes directly to WorkflowHub’s development and governance. This contribution forms part of an ongoing collaboration strategy between BioCommons and ELIXIR to share technical experience and maintain a more global perspective. 

For further details, reach out to us at comms@biocommons.com.au

Conservation managers welcome readymade bioinformatics workflows that support decision making

A small carnivorous marsupial, the Kowari; one of the threatened species that the Galaxy Australia workflows are being applied to.

Conservation decisions are becoming better informed by important genetic information thanks to a new set of bioinformatics workflows that assemble and annotate reference genomes for threatened vertebrate species. Bioinformaticians and conservation managers alike are now effortlessly customising and executing these tailored workflows to conduct sophisticated analyses without extensive computational knowledge. 

The Threatened Species Initiative (TSI) has worked intensively with Australian BioCommons to overcome the barriers that limit the uptake of genetic data into conservation management programs. As part of TSI’s mission to improve conservation practices, a new suite of resources facilitates the easy generation of high quality genetic resources for downstream analyses in situations when a lack of bioinformatics knowledge or access to large-scale compute would have previously made it impossible. 

Making use of the user-friendly ‘point and click’ Galaxy Australia interface, new workflows for genome assembly, data quality control, transcriptome assembly and annotation are easy to use and come with detailed instructions.  By incorporating other BioCommons infrastructure like the Australian Fgenesh++ Service, the workflows are readily available at no cost to Australian researchers and conservation managers. The Galaxy Australia team tailored each step with the tools and compute resources that TSI bioinformaticians and conservation managers would need, and have made it all accessible via the Genome Lab.

Detailed “how-to” guides are already enabling collaborators at Museums Victoria to assemble the genome of the Victorian grassland earless dragon without requiring additional assistance. The detailed instructions are supporting insights into a range of interesting native species, as Patra Petrohilos, PhD candidate in the Australasian Wildlife Genomics Group at The University of Sydney, attests:

“I recently used the Galaxy Australia how-to-guide to help me through the process of reference assembling for the Kowari (a small carnivorous marsupial). I found the instructions incredibly clear and easy to follow and the entire workflow was completed in a few days.”

Development of the workflows and “how-to” guides was led by Dr Luke Silver, Postdoctoral Bioinformatician in the Australasian Wildlife Genomics Group at The University of Sydney, and Dr Anna Syme, Bioinformatician at Australian BioCommons. Luke will present this work at the Genetics Society of Australasia 2024 Conference. 

The workflows are available for anyone to use in WorkflowHub as assembly and annotation collections. The suite of complementary “how-to” guides are easily accessible in BioCommons’ How-To Hub. Prof Carolyn Hogg, TSI Science Lead & co-lead of the Australasian Wildlife Genomics Group at the University of Sydney, expects the resources to be widely applicable:

“The workflows have been built and designed to make genome assembly and annotation simple and easy, enabling the whole Australian life science community to use them.”

The TSI is now calling for new partnerships to extend their range of targeted threatened species, including to insects and invertebrates. If your team’s project focuses on  a target species where genetic information could support conservation efforts, visit the TSI website to apply for partnership before 19 July.

Join the Australian Outpost of BioHackathon Europe 2024!

Are you interested in joining this year’s BioHackathon Europe, but can’t face the long haul flights? You should join the Australian Outpost team who will gather to work locally, while checking in regularly with our international colleagues.

This is a unique opportunity to participate in a significant global event and network with your international peers while working intensively on practical bioinformatics challenges. We will cover your costs when you come to Brisbane for the duration of ELIXIR’s BioHackathon: 4 Nov to 8 Nov 2024. Participation will require an afternoon session plus some work in the early evening to facilitate linking up live with the team in Barcelona. We always make it fun, and you’ll get to know others from around Australia while you learn new skills.

We’ve narrowed down the projects we’re interested in, and want to hear what you want the Australian Outpost of the BioHackathon to work on: 

• Data Model Converter: Bridging Cohort Information Across Biomedical Data Models

• Development of FAIR image analysis workflows and training in Galaxy

• Reducing the environmental impact of Galaxy

• Integrating Bioconductor packages with the ELIXIR Research Software Ecosystem using EDAM

• Enhancing multi-omic analyses through a federated microbiome analysis service

• Executable metadata mappings to FAIRify Biodiversity Genome Annotations

BioHackathon aims to:

• Advance the development of an open source infrastructure for data integration to accelerate scientific innovation

• Engage technical people in the bioinformatics community to work together on topics of common interest

• Strengthen interactions, establish and reinforce collaborations through hands-on programming activities.

Please contact us if you are interested in joining the Australian Outpost of the BioHackathon Europe, and tell us which project/s you would like to participate in, and why. You can read last years’ wrap up and a blog post on why attending is so valuable for inspiration. Once we get a feel for who is interested, we will select a team of people and organise our meetup. There’s no need to register for a place on the BioHackathon Europe website - they have reserved places for the Australian Outpost.

Please submit your expression of interest to comms@biocommons.org.au by 9 Aug 2024.

Improving access to bioinformatics tools and software in Australia

Finding the right computational tools or software for your research can be frustrating. Which tools do what, where can you find them, and which high end computers can you access? 

Since 2021, Australian BioCommons has worked with our infrastructure partners to pull together a convenient list of the tools and software that are available to Australian life science researchers. As part of our ongoing efforts to facilitate simple access to and reuse of existing digital research infrastructure, the Bioinformatics ToolFinder offers a landscape view of what’s out there already. 

ToolFinder has undergone significant ‘under the hood’ changes to make your life easier. ToolFinder 2.0 allows you to filter by research topic according to EDAM ontology, plus free text search across the whole table for tool names, descriptions, licence types, and compute providers. You can even customise your personal view of ToolFinder by adding or removing columns from the table. 

Only looking for tools that have a container? Be sure to use the BioContainers column in your view. Already know the particular tool you need for your analysis? You can search for the tool’s availability and find which versions are installed at various computational facilities. Is your favourite tool not installed where you need it? Not to worry, ToolFinder 2.0 has links for you to request tool installation across Galaxy Australia, NCI, Pawsey and QRIS-Cloud. 

With all these search and sorting improvements made, you’ll quickly narrow down to the tool or software you need among the 600+ entries.
Visit the refreshed ToolFinder now, and let us know how it goes!

BioCLI: Improving command-line infrastructure for life scientists

Australian life scientists are set to be empowered with the resources, skills, and knowledge required to access command-line infrastructure for bioinformatics research through the newly established BioCLI Project. 

Data analysis in the life sciences is constantly evolving, as new instrument types are rolled out and larger amounts of data are generated. The flexibility, scalability, and control uniquely afforded by the command-line interface (CLI) gives users powerful capabilities to interrogate their data, meaning that coding skills can sometimes be essential to particularly complex data analyses. However, the sheer number and diversity of bioinformatics data, tools, and working scales presents a significant entry barrier to using the CLI for life scientists.

Australian BioCommons has established the BioCLI Project to uplift life scientists and help tackle the challenges of working at the CLI, offering environments and services that will reduce friction for processing and analysis of molecular data at scale. Working with our partners at Sydney Informatics Hub, the National Computational Infrastructure (NCI), and the Pawsey Supercomputing Research Centre, BioCLI will:

• Develop key CLI infrastructure such as public virtual machine images that come preconfigured with all the essentials for life sciences research (eg. the BioImage)

• Accelerate command-line job throughput by configuring key tools and workflows to run efficiently on specialised hardware or queuing systems (eg. configuration of Parabricks for NCI’s Gadi supercomputer)

• Provide clear documentation for accessing and configuring all BioCLI outputs

• Have a strong focus on empowering researchers through a dedicated training program

Keep up to date with the latest BioCLI project developments on our website, and be sure to register for our upcoming entry-level webinar “What exactly is bioinformatics?” delivered by Dr Georgie Samaha, Product Owner of BioCLI and Bioinformatics Group Lead at the Sydney Informatics Hub, The University of Sydney.

Galaxy Australia leads 2024 Galaxy Project publication

The latest developments in the Galaxy platform have been captured in a definitive publication describing the popular international data analysis platform. Lead author and Project Lead of Galaxy Australia, Dr Gareth Price, coordinated the paper that documents the key features supporting accessible, reproducible, and transparent user-driven research.

Gareth was proud that The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update highlighted several key features that will particularly benefit Australian researchers:

“One exciting new offering is Galaxy Australia’s Genome Lab, which presents a customised, user-friendly view with rapid access to a range of sophisticated resources tailored for genome researchers. Our locally developed features are now available for researchers around the world to use.”

Galaxy Project spans the globe, with over 500,000 individuals registering an account across the 19 years of operation. It is a collaborative community of dedicated contributors, working to constantly improve the service while following core values of supporting accessible, reproducible, and transparent user-driven research.

Leading the biennial Galaxy Project publication in the 2024 edition of the Nucleic Acids Research’s annual Web Server Issue was a rewarding experience for Gareth:

“It was a privilege to lead such an impactful publication that now becomes the citable entity for any researchers using Galaxy, particularly after the 2022 publication had 490 citations and over 16,000 views in only two years. And what a wonderful opportunity to collate Galaxy’s progress through the contributions of over 120 authors globally and their efforts in feature development for Galaxy users.” 

In all, 19 Australians contributed to the paper, representing the important input of Galaxy Australia to the global research community. The Galaxy Australia team has been instrumental in delivering service optimisations like the Total Perspective Vortex, and feedback from Australian users has driven user experience improvements internationally. 

The publication also highlights the addition of licensed bioinformatics tools Fgenesh++ and Cell Ranger to Galaxy. These powerful software packages are fully subsidised for Australian researchers to use, and through their enthusiastic use, the Galaxy team hope to build a body of evidence that encourages software developers to consider providing both open and commercial licensing options to meet researchers’ needs. Further improvements across user accessibility, self-guided training via the Galaxy Training Network, and back-end technical aspects to ensure jobs continue to run smoothly are also detailed in the publication.
Galaxy continues to evolve based on the needs of the open research community. With the release of this publication, and many new features to explore, there’s never been a better time to get started using Galaxy!

ZERO Childhood Cancer Data Portal launched

Researchers can now access a large bank of paediatric genomic data collected as part of the ZERO Childhood Cancer program, including molecular, phenotypic, multi-omics, and clinical data, plus physical biospecimens across 38 diseases. Housed within the newly launched ZERO Childhood Cancer Data Portal, the datasets represent tumour samples from 1,019 participants in the ZERO2 clinical trial, which includes all children with cancer in Australia and Aotearoa/New Zealand.

The Human Genome Informatics team at the Australian BioCommons was thrilled to recently partner with the Children’s Cancer Institute (CCI) and the ZERO program to support their efforts in establishing the data portal, which formed part of a national, multi-institutional project called the Human Genomes Platform Project (HGPP). The HGPP was designed to enhance capability for securely and responsibly sharing human genome research data nationally and internationally, ensuring maximum value can be derived from these assets. Along with CCI and ZERO, HGPP was a successful partnership between Australian Access Federation, Australian BioCommons, Australian Genomics, Garvan Institute of Medical Research, National Computational Infrastructure, QIMR Berghofer Medical Research Institute, and University of Melbourne Centre for Cancer Research. 

The HGPP team adapted GA4GH’s Beacon network for implementation in Australia, with Beacon v2 now supporting the ZERO Childhood Cancer Data Portal. To learn more about key outcomes and outputs of the HGPP, watch the final showcase on the BioCommons YouTube channel.

The development of the ZERO Childhood Cancer Data Portal was supported by the Australian BioCommons' Human Genomes Platform Project and funded through NCRIS investments from Bioplatforms Australia and the Australian Research Data Commons, and investment by the ZERO Childhood Cancer Program and Children's Cancer Institute.

Reducing the frustrations of research data movement

Researchers' problems inform everything BioCommons does. We seek out researchers, institutions and research consortia willing to share their roadblocks, annoyances and limitations. Designing solutions to these challenges that enable researchers to do their best work without impediments requires connecting the right people across Australia’s digital life science research landscape with the best international efforts. 

Collaborating locally

As the bioinformatics capability of Bioplatforms Australia, we regularly collaborate with other BPA-funded facilities. When the national Biomolecular Resource Facility (BRF) expressed an urgent need for faster data transfer to their research customers and collaborators, we listened very carefully to their sources of frustration. The sheer size of their data movements had seen their team even resorting to delivering physical hard drives in the past!

After understanding the requirements, we identified AARNet, the operator of Australia’s national research and education network dedicated to moving research data, as being well placed to solve this problem. AARNet’s Digital Research Product Manager Greg D’Arcy collaborated with BioCommons to create a solution.

Making the right connections between people, facilities and services can lead to wonderful efficiencies in data movement, and AARNet recently described how BRF is now efficiently and safely transferring vast amounts of data overseas, and without any risk of data loss: Data Without Borders: the role of Globus in international genome research. As Globus’ partner for universities and research institutes in Australia, AARNet was key to implementing this data management tool into an elegant workflow. Data that is transferred directly from BRF instruments to the National Computational Infrastructure (NCI) for processing and storage can now be seamlessly transferred to recipients with their own Globus endpoints.

Collaborating internationally

Another example of seeking out researchers’ opinions is our ongoing call out for individuals with an interest in data submission to international repositories. Our community consultations have already teased out some of the challenges faced by Australian-based researchers in the data submission process and we have published a set of recommendations to address them.

As part of a range of activities around interfacing with international omics data repositories, BioCommons is investigating the value of bringing European Bioinformatics Institute (EMBL-EBI) / European Nucleotide Archive (ENA) team members to Australia. To facilitate improvements by connecting the right people, we are exploring various opportunities, with training workshops for data submission to ENA, sessions to provide feedback on existing ENA documentation, and collaborations around documentation all up for consideration. 

We’d love to know what you think of these opportunities to interact with the ENA team and if you’d like to participate! Please complete our survey by 14 June 2024.

To contribute to the conversations in your area of interest, join one of our research domain focused mailing groups to hear about future consultations and events.