New community uplifts bioinformatics trainers in Australia

Australian BioCommons is launching a new community to uplift bioinformatics trainers in Australia. The National Bioinformatics Training Cooperative brings together training providers, managers, and (current and aspiring) trainers from research organisations, universities and infrastructure providers around collaborative events that connect trainers and create new opportunities in bioinformatics training.

In our first community event on Friday 21 July, Dr Katharina F Heil, Programme Manager Communities & Training for the European life sciences infrastructure (ELIXIR) joins us to share her reflections on:

• What makes a successful research infrastructure community?

• What are the roles that engagement and training play in building communities of users and developers around research infrastructures?

• What opportunities exist to maximise collaboration between organisations, to foster engagement with researcher and developer communities?

• What future community and training opportunities are on the horizon?

There will be plenty of time to ask Katharina questions and discuss the topic with other attendees. Registrations are essential.

Find out more about how you can benefit from being part of the cooperative and sign-up for the ‘The runsheet’ newsletter to stay informed about community activities, news and opportunities for trainers.

Australian BioCommons and ELIXIR announce extension of collaboration strategy to 2028

Celebrating the collaboration strategy at the All Hands Meeting 2023. Left to right: Gareth Price, Service Manager (Galaxy Australia), Niklas Blomberg (ELIXIR Director),  Jeff Christiansen (Australian BioCommons Deputy Director), Katharine Heil (ELIXIR Programme Manager Communities and Training), Corinne Martin (ELIXIR Programme Manager - Impact and International), Peter Maccallum (ELIXIR Chief Technical Officer), Frederik Coppens (ELIXIR Belgium), Björn Grüning (ELIXIR Germany).

ELIXIR, the European life science data infrastructure, has renewed its collaboration strategy with Australian BioCommons, its Australian counterpart. Both organisations work to further open access to resources to understand the molecular basis of life and have been collaborating for many years, leading an original collaboration strategy in 2020.

Renewing of the strategy, signed in April 2023, was formally marked at an in-person gathering at the ELIXIR All Hands meeting in Dublin last week, which included a plenary presentation by Australian BioCommons Deputy Director, Jeff Christiansen. 

The mutually beneficial strategy has been extended until 2028 and builds on the successes of the last three years to further share technical experience between the infrastructures, along with giving both organisations a more global perspective.

The collaboration will continue to use a range of activities including reciprocal invitations at signature meetings, working together to create special sessions at key bioinformatics events, closer linkages and interactions on existing mutually beneficial activities, study visits by ELIXIR and Australian BioCommons experts, and staff exchanges.

Notable achievements:  2020 to 2023

During the past three years, there have been achievements in five technical areas, selected examples are listed below.

Training

• Exchanged best practices in training between the BioCommons Training team and the ELIXIR Training Platform

• Leveraged the ELIXIR TeSS (Training eSupport System) codebase and technical architecture for the development of DReSA (Digital Research Skills Australasia). In turn, sharing the code base from DReSA back with TeSS

• Established the first Australian outpost for BioHackathon Europe 2022, with in-depth contribution across time zones.

Tools (including Galaxy)

• Jointly improved the Galaxy Project ecosystem through deployment of AlphaFold, an improved job scheduler and internationalisation of Galaxy’s Training Infrastructure as a Service

• Collaborated on best practice and training in bio.tools, EDAM ontologies, containers and performance benchmarking

• Adopted WorkflowHub as an Australian national workflows registry (now with 47 workflows, 6 partner organisations, 69,831 views, 467 downloads)

Compute and AAI (Authentication and Authorisation Infrastructure)

• Incorporated learnings from a study tour into the BioCommons AAI project, including the Authentication and Authorisation for Research and Collaboration (AARC) blueprint architecture

• Shared knowledge with ELIXIR on commercial cloud as BioCommons upgrades the national Nextflow tower

• Exchanged expertise on the BioCommons ABLeS program (enabling access to Australia’s Tier-1 high performance computing centres) as an exemplar providing compute access within a lightweight policy framework

Data (including human data)

• Jointly chaired the Research Data Alliance (RDA)’s Life Science Data Infrastructures Interest Group

• Shared expertise around enabling more efficient data publishing and re-use in a global context

• Explored establishing a federated node of the EGA in Australia, with the BioCommons Human Genome Informatics team joining ELIXIR’s Federated Human Data Community 

Forward facing: 2023 to 2028

Looking to the future, ELIXIR and the Australian BioCommons aim to build on the successes of the past three years in the areas of training, tools, and compute deepen existing partnerships between corresponding ELIXIR and BioCommons communities. New links will be developed with the ELIXIR Data and Interoperability Platforms and in a wider range of special interest groups, including the nascent ELIXIR Biodiversity and Research Data Management (RDM) Communities.

There is a renewed commitment to face-to-face interactions, including longer visits and staff exchanges. These kick off with an ELIXIR delegation, from both the ELIXIR Hub and Nodes, travelling to Brisbane for the Galaxy Community Conference in July 2023 and staying on after the meeting to build in-person links across both infrastructures.

Find out more

ELIXIR and Australian BioCommons Collaboration Strategy 2023-28

ELIXIR’s International Strategy

ELIXIR and Australian BioCommons training collaborations

Contacts: ELIXIR (Corinne Martin), Australian Biocommons (Christina Hall)

Cultivating community management skills with the Center for Scientific Collaboration and Community Engagement

From consultations with life scientists to developing infrastructure, community and collaboration are core to what the BioCommons and our partners do. That’s why BioCommons recently contracted US specialists in the engagement of scientific communities to deliver training to the Australian research infrastructure workforce.

The Australian BioCommons team and partners from Australian Research Data Commons (ARDC), Bioplatforms Australia, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Australian Genomics, University of Melbourne Centre for Cancer Research (UMCCR), and the Australian Access Federation (AAF) recently joined the Center for Scientific Collaboration and Community Engagement  (CSCCE) for an Australian-timezone friendly offering of their popular Community Engagement Fundamentals course. 

This eight week professional development opportunity recognised and consolidated the (often invisible) skills our engagement teams bring to our collaborative projects and provided frameworks that we are now using to plan for our own scientific communities. 

We loved the interactive way that the course got us talking and thinking about how we create space for our communities to flourish. The course left us feeling energised, inspired and more confident in our work as community managers.

“I now appreciate the enormous and highly diverse skill sets required to undertake a community manager role. I’m embracing that it will take time to develop a true community for my project and enjoying the ride!” - Sarah Thomas, AAF

Weekly readings, resources, frameworks and activities helped us think deeply about our communities and put new skills into action. 

“Understanding the community life cycle and the community participation model were an eye opener for me. My community is still in the ideation stage and the course was a great help to form my opinions/strategies about what needs to be done.” - Farah Zaib Khan, Australian BioCommons

The chance to discuss and think out loud about our communities with others was equally as valuable. Even though the course is now finished we plan to keep meeting up to share ideas and support each other in our community management roles.

“It was liberating to have so much time to think about my community and their needs and to talk this through with others. This helped generate a new focus for my community that will cater for the needs of all of the members” - Andy White, ARDC

CSCCE supports the professionalisation and institutionalisation of the community manager role within science. Find out more about their research, courses and consultancy offerings, as well as their international community of practice for STEM community managers.

National collaboration advances computing power for bioinformatics

Australian BioCommons has entered into an access agreement with the Pawsey Supercomputing Research Centre boosting access to high end supercomputing for life science research nationally. The partnership offers life science researchers an unparalleled level of access to high-end supercomputing resources, including 10 million core hours of supercomputing, cloud, GPU, and data services, as well as comprehensive support and help desk assistance.

The agreement between the BioCommons’ lead agent, the University of Melbourne, Pawsey and CSIRO will make Pawsey's state-of-the-art resources more available than ever before to life scientists across the country.

“By providing biologists with flexible access to powerful computing resources, we are breaking down a major barrier to scientific progress. This agreement formalises our longstanding relationship and empowers the bioinformatics community, encouraging bioinformatics researchers to take advantage of high-performance computing resources.”

Dr Sarah Beecroft
Life Science Applications Specialist, Pawsey Supercomputing Research Centre

Australian BioCommons will directly manage these projects, initially activating access through the Australian BioCommons Leadership Share (ABLeS). Pawsey’s recent HPC technology refresh also offers new impact-focused schemes and additional resources for eligible researchers, offering even greater potential for innovation and impact.

Galaxy Australia goes warp speed: 6 million jobs, new features and the team goes to GCC2023!

Over 6 million jobs have been submitted and more than 75,000 workflows have been run on Galaxy Australia by researchers, demonstrating the platform's immense value in facilitating research across a range of fields. 

It’s not just researchers who’ve been getting busy with Galaxy. Behind the scenes the highly skilled Galaxy Australia team has been improving the user experience, building a new Genome Lab focused on the needs of Australian genome assembly and annotation researchers, and developing new tools for better managing the Galaxy service nationally and internationally.

Team members from Queensland Cyber Infrastructure Foundation (QCIF), Australian BioCommons, University of Queensland, The University of Melbourne and AARNet are also getting ready to join the Galaxy Community Conference from 10 - 16 July in Brisbane to share their knowledge and learn from the community.

Topics that the team will present on include:

• Galaxy Australia - soliciting user feedback to improve user experience (Madeline Bassetti, Winnie Mok, Gareth Price)

• Galaxy Australia History Mailer (Catherine Bromhead, Thom Cuddihy, Simon Gladman)

• Galaxy subdomain development for the Australian genomics community (Anna Syme, Cameron Hyde, Madeline Bassetti, Winnie Mok, Gareth Price)

• Enhancing Remote Data Access in Galaxy by Unifying URL Handling and Filesource Capabilities (Nuwan Goonasekera, Uwe Winter)

• A process for monitoring tool health on Galaxy Australia (Cameron Hyde, Tom Harrop and Mike Thang)

• Powering Galaxy Australia into the Future – AARNet supporting large-scale, collaborative computational science (Olivier Allart)

There’s still time to join the community at GCC to hear about the latest Galaxy developments, learn new skills and share knowledge with the Galaxy community.

Poster abstracts and applications for virtual fellowships close on 2nd June.

Find out more and register 

Local conference striving to make data analysis easier

Thousands of Australian researchers are using the free Galaxy Australia web platform for their data intensive science. The long-standing BioCommons service is trusted by researchers to build, run, share, and repeat their own complex computational analyses using only a web browser - without having to learn to use command line interfaces or worry about system administration.

The annual meeting of the global Galaxy community is coming to Brisbane in July, offering a great chance to learn more about Galaxy, how people are using it for their research, and what goes on behind the scenes with Galaxy infrastructure. There are plenty of opportunities to learn practical skills, get involved in the open-source development of the platform, or give direct feedback to Galaxy developers on what your research needs!

This friendly and inexpensive conference uniquely welcomes both biologists and software developers. The Galaxy Community Conference (GCC2023) will showcase the latest in Galaxy advanced capabilities, demonstrate how researchers are using Galaxy and offer training in how to use Galaxy for topics including machine learning, microbiology, structural biology and AlphaFold, genomics, genome annotation, genome assembly, single cell transcriptomics and human genetics. 

Local keynote speakers include Assoc Prof Roberto Barrero Gumiel from Queensland University of Technology, who will share how he uses Galaxy to enhance Australia’s plant biosecurity. Dr Carolyn Hogg from the University of Sydney is demonstrating how Galaxy contributes to her research in biodiversity conservation genomics of Australia's native animals. University of NSW structural biologist and power user of the Australian AlphaFold service, Dr Kate Michie, will present insights into how she uses AlphaFold in Galaxy Australia.

The analysis service has grown 10-fold in recent years, enabling national impact in research areas including human and animal parasite structure-based genome annotation at University of Melbourne, biosecurity surveillance and diagnosis at QUT and virus and bacteria genomics at University of Queensland, and resulting in acknowledgements in many peer-reviewed publications.

Head to GCC2023 from 10-16 July to understand how Galaxy Australia can help you get the most out of your data. Or, simply register to join online to hear more.

Find out more and register 

Powering bioinformatics training with (free) computational infrastructure

The computational infrastructure needed to run data analysis training is now readily available at no cost to Australian educators and researchers. Galaxy Australia has a simple offer: you provide the training, we provide the infrastructure and support. Their "Training Infrastructure as a Service”, or TIaaS, makes training simpler to organise and run. Trainers no longer need to provision virtual machines for each trainee nor find a suitable computer training lab. Galaxy Australia is web accessible, allowing trainees to use any web enabled device to access training. 

Trainees get access to the computational power they need and their jobs are optimised to ensure they run quickly. All histories and important data remains accessible on Galaxy Australia after the workshop finishes so new skills can be immediately put to use.

Trainers use a customised dashboard to track their student’s work, allowing for real time control of the workshop progress, whether training in person or remotely. Galaxy Australia administrators also monitor the training event behind the scenes and can fine-tune any resourcing required for the best experience. 

Training materials can be selected from the library of tutorials developed and maintained by the worldwide community on the Galaxy Training Network (GTN), or trainers can bring their own curriculum. The GTN materials are written by experts and are regularly refreshed and highly reliable, so trainers can be confident the tools will work. Galaxy Training materials are being used by educators internationally in a growing range of different learning environments. 

Training support is offered by the Galaxy Australia team and via a friendly international community who are active on lots of different channels and who welcome participation via working groups and collaborative training events like the Galaxy Smörgåsbord. A free online Train-the-trainer workshop covering learning principles and techniques is also being offered by the international Galaxy community in June.

Australian BioCommons workshops have been testing the TIaaS service for some time now. Training and Communications Officer, Dr Melissa Burke, recommends the service to others organising training events: 

“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, Training and Communications Officer
Australian BioCommons

TIaaS recently supported a class of over 70 Protein Chemistry students at La Trobe University to analyse their own proteomics data on Galaxy using the Morpheus database search tool.  

“The students ran their analyses right away and I could see there were no unexplained problems. Thanks to the advice of the Galaxy Australia team I made several public histories ahead of time for the students, giving them quick access to their own proteomics mass-spectra file to work on.”

Dr Rohan Lowe, Mass-Spec Facility Manager (Proteomics)
La Trobe University-Proteomics and Metabolomics Platform

Dr Matt Padula, Director University of Technology Sydney Proteomics Core Facility, also makes extensive use of Galaxy Australia for proteomics training. Alongside his technical support and instrumentation services, Matt regularly uses TIaaS to keep track of concurrent tasks, facilitating his tailored support of individual students.  

TIaaS frees trainers from setting up and maintaining computational resources for their training events. With Galaxy Australia providing the compute and back-end support for data analysis training, trainers can focus on student needs and learning outcomes. All costs are covered by the Australian BioCommons for Australian users.

Apply to use TIaaS for your next training event

Cracking the code of Australia's most invasive species

Dr Rahul Rane (left) and Dr Tom Walsh will sequence hundreds of genomes for the Australian Pest Genome Project

We're excited to partner with CSIRO and Australian Research Data Commons (ARDC) to share the genomic data that will underpin species-specific management of pests & weeds in the future. This important project will soon host the assembled and annotated genomes on the Australian Apollo Service, allowing interactive browsing and collaborative curation. We are proud to support the Australian Pest Genome Partnership as we work towards making genomic data more easily accessible and usable to support industry, government and the scientific community in managing pests.

The story reproduced below New CSIRO project to crack the codes of Australia's most invasive species was recently published on the CSIRO news page.

CSIRO, Australia’s national science agency, has embarked on an ambitious new project to unravel the genetic blueprints of Australia’s top pest and invasive species to better enable their management or eradication.

The Australian Pest Genome Partnership (APGP) will generate the genomic data of hundreds of pests and weeds and make it freely available, along with digital solutions to help analyse the data. The data will assist researchers working on pest and weed species and underpin next generation species-specific solutions.

Invasive species have cost Australia $390 billion over the past six decades, with weeds costing the agriculture sector at least $5 billion a year. This presents a significant burden to Australia’s agriculture and livestock industries, as well as the significant and ongoing environmental impacts created by these invasive species.

APGP has now prepared its first 28 genomic datasets, and this year, with its collaborators, will make public genomic data assets for some of Australia’s top pest and invasive species such as mosquitoes, khapra beetle, cane toad, fall armyworm, fox, feral pig and cat as well as weeds such as wild radish, rye and rat’s tail grasses.

CSIRO principal research scientist Tom Walsh said data is easy but analysis is hard. APGP intends to make genomic data more easily accessible and usable to support industry, government and the scientific community in managing pests.

“This project has the potential to drive new science and digital innovations to safeguard Australia’s environment and biosecurity from existing and growing threats posed by invasive and pest species,” Dr Walsh said.

“In the same way genome sequencing has helped inform medical advice, pest genomes can help us unlock new ways of protecting our environment, agricultural sector and public health with a quick and targeted response.” he said.

CSIRO senior research consultant Rahul Rane said the fit-for-purpose genomics database being delivered through APGP will be a game-changer in invasive species control and management.

“Genomes and genetic diversity data can tell us all manner of things including where a particular pest species has travelled from, what environments it may thrive in, and whether it has developed resistance to chemicals and pesticides,” Dr Rane said.

“The more we know about the genetic characteristics of a pest, the better our ability to make informed decisions to effectively control or eliminate them safely.

“Ultimately research based on these new datasets will benefit all Australians by reducing public health risks and the impact of these pest species on our environment and agricultural production”.

Hundreds more pests are being sequenced this year, including jellyfish, invasive ants and beetles, termites, African boxthorn, crown of thorns starfish, ticks and head lice.

APGP is looking to partner with companies, government departments and other research organisations to continue sequencing and collating the genome of pests impacting Australia’s biosecurity.

The project received investment from the Australian Research Data Commons (ARDC), and has received co-investment from Australian BioCommons and Australian National University. Genomic datasets were developed in collaboration with Macquarie University, University of Melbourne, University of New South Wales, University of Queensland, University of Western Australia, Queensland Department of Agriculture and Fisheries and South Australian Research and Development Institute.

The ARDC and Australian BioCommons (Bioplatforms Australia) are funded by the National Collaborative Research Infrastructure Strategy (NCRIS).

Visit Australian Pest Genome Project to learn more, or contact the team to access the data.

New podcast: Meet the RDA Life Sciences Infrastructure Interest Group

Our own Dr Jeff Christiansen has been featured on a podcast in a discussion about research data management. As well as being the BioCommons’ Deputy Director and A/Director: Engagements and Operations, Jeff is a Chair of the international Research Data Alliance’s Life Sciences Infrastructure Interest Group who were invited to share what challenges, and potential impacts and outputs the group is working towards.

The Data Streams Podcast is a collection of conversations among members in the RDA community about challenges they face as researchers and data experts in managing the massive quantities of research data and how together, they are finding solutions and proving the value of open research data sharing and reuse.

Stay up to date with what is happening with Research Data Management by subscribing to the RDA Data Streams Podcast.

Realising 'BYO data' goals

The BioCommons and ARDC sponsored BioCommons ‘Bring Your Own Data’ Expansion Project is delivering a key component of BioCommon’s vision for an ecosystem of data analysis and digital asset stewardship platforms. We've just added a new page to our website that details our achievements to date, and what continues to keep us busy across the project’s various activities.

• Web-based bioinformatics workbenches
  Online access to best-practice life science tools, workflows, data and training, underpinned by compute and storage that we manage for you

• Command line for life scientists
  Community curated life science workflows, tools, training and support across Australian command line infrastructures

• Data infrastructure for life scientists
  Making it easier for life scientists to access, analyse, visualise and share data coming from data generating facilities, or generated by research consortia.

Check out the progress and future plans