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

Join us in Brisbane for GCC2023!

The international Galaxy Community Conference (GCC) 2023 is finally coming to Australia in July.

GCC2023 will bring together hundreds of researchers, trainers, tool developers, software engineers, and computational infrastructure providers, from all over the world. This unique meeting of back end developers, service deployers and research users offers a range of ways to exchange information about using the Galaxy data integration and analysis platform for data intensive science.

It's a friendly, fun meeting that provides a great opportunity to get to know this welcoming open source community. BioCommons and Galaxy Australia and the rest of the Organising Committee are working hard to keep the event diverse, interesting and inexpensive.  

GCC2023 registration now open

Learn new biological data analysis skills at this free online global training event

The Galaxy Training Network is happy to announce the 3rd annual edition of the GTN Smörgåsbord global training event. This 5-day, 24/7 training event is completely free, and covers a wide range of topics, including foundations of data science, genomics, proteomics, machine learning, single-cell analysis, metagenomics, cancer analysis, SARS-CoV-2 analysis, ecology, climate science, RO-crates, and much much more!

During the week, YOU decide your own schedule, pick and choose the topics that are interesting to you, and learn at your own pace, with support from the global community of over 100 Galaxy instructors available on Slack 24/7 to answer your questions - including the team from Galaxy Australia who will be available to answer your questions whenever they come up.

 When: May 22-26, 2023
 Where: Online
 Format: Asynchronous, choose-your-own-adventure, video tutorials with online support
 Price: Free
 Program & Registration: https://gxy.io/smorgasbord3

Registration is now open (the program is still being updated, so check back regularly for the latest additions to the program).

The Galaxy Training Network

P.S. Feel free to join our Slack (invite: https://gxy.io/smorgasbord-slack) already, we will post the latest updates here, and of course we are happy to answer any questions you may have about the course.

Creating healthy research data ecosystems in the cloud

The rise in global usage of Gen3 to manage, analyse and share research data called for the creation of an international community to share knowledge. BioCommons partnered with the Center for Translational Data Science, University of Chicago, USA late last year to co-host the inaugural Gen3 Community Forum, and the first event of 2023 will take place online 2 Mar 2023 (or 1 March for our US colleagues!).

How to Set Up a Gen3 Data Commons Using Helm Charts will provide guidance in standing up, configuring, and maintaining your own Gen3 Data Commons in multiple clouds by using Helm Charts. The tool streamlines the installation and management of Kubernetes applications, which is a system for automating deployment, scaling, and management of containerized applications.

The Gen3 platform consists of open-source software services that support the emergence of healthy data ecosystems by enabling the interoperation and creation of cloud-based data resources, including data commons and analysis workspaces. Gen3 aims to accelerate and democratise the process of scientific discovery by making it easy to manage, analyse, harmonise, and share large and complex datasets in the cloud.

Gen3 is now a key component over 15 data commons by organisations including several NIH Institutes and Centers in the USA. Working with the Gen3 team BioCommons is supporting the creation of several data commons for Australian research consortia.

Register and learn more about the Gen3 Community

See related BioCommons stories:

Supporting Australian cardiovascular research

Webinar: Establishing Gen3 to enable better human genome data sharing in Australia