Galaxy Australia’s uptake reaches a new milestone: 7 million jobs and counting!

Kylie’s class celebrate submitting Galaxy’s seven millionth job

When the seven millionth job was submitted to Galaxy Australia, we were excited to see what area of research had triggered this milestone.  The lucky job was submitted by a student in Dr Kylie Munyard’s undergraduate course ‘Introduction to Bioinformatics’ at Curtin University. 

As Senior Lecturer in Molecular Genetics within the Curtin Medical School, Kylie regularly uses the extensive training materials available in Galaxy Training to teach her graduate researchers and undergraduate students how to use a wide range of data analysis tools: 

“It is intuitive to use, it’s easy because students don’t have to install software, it has lots of really good documentation and visualisation, and all of this helps the students to understand what they are doing and more importantly why they are doing it.”

This university course teaches students how to import their raw sequence read data and move through a standard workflow of assembling genomes, calling variants, creating annotations and studying gene expression using Galaxy Australia. 

Another key feature of Galaxy Australia that makes life easy for computational life science trainers is TIaaS (Training Infrastructure as a Service), or as Kylie describes it: “A little ‘corner’ of Galaxy Australia dedicated for our class use.”

TIaaS provides dedicated compute power, customised dashboards, and tracking of trainee jobs. All Australian trainers are eligible to use TIaaS through a simple application process, which can include setup assistance and backend support during training events. Trainers capture important technical event reports and trainees can access their data after the event for continued learning. 

Rapid uptake of Galaxy Australia by researchers, trainers and trainees demonstrates the platform's versatility across a range of fields. Its popularity amongst bioinformatics teachers is just one of the reasons that it has been only a few months since Galaxy Australia celebrated reaching 6 million jobs! 

Check out the wide range of tutorials available in Galaxy Training, and investigate how TIaaS can support successful training events.

A purpose built environment for bioinformatics on the command-line

A new welcoming interface to high performance computing environments has been created specifically for bioinformatics users. The “BioImage” comes pre-installed with software, tools and datasets commonly used in the bioinformatics domain.

The BioImage has been purpose built to help researchers working on the command-line, removing the need to invest time in installing common software such as Singularity, Jupyter Notebook, RStudio or Nextflow. Researchers can follow bioinformatics best practices without having to set up the environment themselves from scratch, providing a reliable and reproducible starting point for new projects. 

The BioImage is already in use on the Pawsey Nimbus Research Cloud and has detailed instructional documentation available. Its collaborative development has been led by Audrey Stott, Systems Administrator at the Pawsey Supercomputing Research Centre, as part of the BioCommons ‘Bring Your Own Data’ project. The utility of the BioImage will see it made available at other national HPC facilities, and work is currently underway to ensure compatibility with NCI’s Nirin Cloud. Expect to see it rolled out across other facilities in the near future.

Two particularly exciting features of the BioImage are CernVM-FS and Singularity-HPC. CernVM-FS is a mounted shared file system that provides users access to over 8,000 Biocontainer tools, plus common reference data sets. Singularity-HPC (a container-specific software module) then makes users’ lives easier by enabling them to execute containers as modules, bypassing the need for container syntax.

BioCommons bioinformatician Dr Georgina Samaha has assisted numerous University of Sydney researchers to use the BioImage in her role as Bioinformatics Group Lead at the Sydney Informatics Hub. Alexandra Boyling, PhD candidate at the ANZAC Research Institute said:

“The Bioimage was a great place to enter the world of bioinformatics and really helped me to upskill on the command-line. I was able to jump right in and make use of Nextflow pipelines, Singularity containers and interactive Rstudio sessions. As a wet-lab scientist, I felt quite intimidated by the idea of analysing the vast volumes of genomic data I was working with. Now I feel considerably more confident, and even excited, about the prospect of incorporating more bioinformatics into my projects in the future."

The BioImage is also proving useful for group training, providing all trainees with access to a consistent computational environment with everything pre-loaded and ready to go. When used with Pawsey’s powerful Nimbus compute, it presents a friendly gateway that is tailored for bioinformatics jobs, and includes a risk-free sandbox to work within. Using the BioImage for training means that learning takes place in an enduring environment that can be returned to over time once paired with a (quick and easy to get) allocation to Pawsey’s resources. Trainees attending the upcoming online BioCommons workshop ‘RNASeq: reads to differential genes and pathways’ will no doubt continue to use the BioImage well after the training event is over.

Read more about the BioImage

Powering up the ACDC

The Australian Cardiovascular disease Data Commons (ACDC) will pave the way for researchers to make new mechanistic insights and identify potential markers for coronary artery disease (CAD), plus facilitate a translational pipeline to ensure new discoveries are deployed to clinical practice. A new comprehensive, secure, scalable, and internationally integrated data infrastructure will provide access to pooled data from approximately 400,000 individuals across up to 18 clinical cohorts within Australia. 

CAD is the most common type of cardiovascular disease, both in terms of deaths and hospitalisations. Despite developing over several years, CAD is difficult to detect and many patients have no warning symptoms. Developments in data-intensive biomarker research techniques such as genomics, metabolomics, proteomics and immuno-phenotyping, paired with advances in image processing, machine learning, and systems biology pipelines, present opportunities to better understand and identify those at risk through pooled analysis using research infrastructures such as the ACDC.

Work on the ACDC commenced in September, with all stakeholders in the MRFF Critical Research Infrastructure Grant meeting online, including representatives of all 18 clinical cohorts that are planned to be integrated into the ACDC platform. 

It’s a long way to the top, and small working groups will now hold fortnightly ‘sprints’ to keep the ACDC moving forward. You can read more about the ACDC on the BioCommons website.

A formal, in-person, kick off of the ACDC will occur in early December as part of a broader Australian Cardiovascular Alliance Precision Medicine Flagship event hosted by the Baker Heart and Diabetes Institute.

The ACDC project is led by the Baker Heart and Diabetes Institute and funded by the Medical Research Future Fund (MRFF) and Bioplatforms Australia (MRFF 2022 National Critical Research Infrastructure Grant: Building an Australian Cardiovascular disease Data Commons). Additional contributions are being made by the Baker Heart and Diabetes Institute, 23Strands, ACvA, CSL Limited, University of Sydney, Australian BioCommons, data custodians and other partners.

Spotlight on Research Software Engineers

TheRSEAA2023 unconference in action. Clockwise from top left: Aleem Uddin (ARDC), Saranjeet Kaur (RSEAA2023 Organising Committee), Johan Gustafsson, Steven Manos.

The Research Software Engineer Asia Australia (RSEAA) unconference and the New Zealand Research Software Engineering conference have just wrapped up their back-to-back programs for 2023. Australian BioCommons supported these important events, and thought you might like to know more - particularly if you’ve not heard of a Research Software Engineer (RSE) or an unconference before!

Australian BioCommons was proud to be a key partner of the RSEAA2023 unconference, particularly with this year’s theme ‘Silos to Synergy - Achieving collaboration across domains’. Dr Steven Manos, Associate Director of Cyberinfrastructure at BioCommons said:

“We were able to have thoughtful and creative discussions with people representing different disciplines from around the Asia Pacific region. It was great to hear voices we might not come across at more traditional conferences.”

Australian BioCommons also coordinated a Birds of a Feather (BoF) session at the NZ Research Software Engineering Conference. Dr Johan Gustafsson, Bioinformatics Engagement Officer at BioCommons, led the discussion on development of the AU-NZ bioinformatics software accelerator, a collaborative effort between Australian BioCommons (through ABLeS), Pawsey Supercomputing Centre, New Zealand eScience Infrastructure and the National Computational Infrastructure Australia. Johan said:

“The BoF attendees were excited by the software accelerator concept, particularly for potential support in migrating their code to high performance computers, and sharing knowledge with other Research Software Engineers (RSEs) undertaking similar work. We’ll help RSEs make the most of their allocations in a high performance, but low pressure environment. Stay tuned for more on the software accelerator in early 2024!”

What is a Research Software Engineer?

Research Software Engineers (RSEs) are people who combine professional software expertise with an understanding of research. The RSE Association of Australia and New Zealand define RSEs as researchers/academics who code, generalists who bring communities together across the research and technical domains, systems administrators who maintain research systems, and software engineers who work in the research space. RSEs are critical team members that are often challenged in terms of unclear career progression, difficulty meeting typical academic metrics and a lack of recognition for their contribution to research progress.

What is an unconference?

Unlike a typical academic conference, an unconference crowd sources the abstract selection process. All delegates can suggest topics for discussion, everyone can vote, and the most popular topics are discussed. This democratic approach provides an opportunity for diverse voices to be heard, particularly those often left out in the regular conference selection process. You can read more about the unconference philosophy on Wikipedia.

How does an unconference support diversity and inclusion?

The lack of a formal program during the unconference lowers the barrier to participation and provides an opportunity for everyone to speak. Delegates can advocate for their interests by suggesting and voting for topics, and a focus on networking and career progression helps to build a welcoming and supportive community. You can read more about making an inclusive unconference in this Times Higher Education article.

The virtual delivery of RSEAA2023, with minimal frills to keep costs down, removed the requirement to travel, reduced registration fees, and made live captioning possible. RSEAA2023 also offered scholarships covering the registration costs, plus accessibility microgrants that could be accessed to cover smaller costs of attending, eg. childcare for the day or a pair of headphones to listen in virtually.

Want to know more?

• If you’re not sure if you identify as an RSE, this list of questions from the UK RSE association could help

• If you’re interested in RSE careers you can:

• Read the Australian Research Data Commons (ARDC) profile of Catherine Bromhead, software developer at the Australian BioCommons and Melbourne Bioinformatics

• Read more career profiles on the RSE AU/NZ site

• If you’re an RSE looking to contribute, join the ARDC Visible Research Software interest group. The group is co-hosted by Dr Johan Gustafsson and aims to improve research software recognition by ensuring it is visible, cited, published and FAIR

• Read a Ten Simple Rules publication on organising an unconference.

International collaboration has local impact: ELIXIR comes to town

Members of the BioCommons team with ELIXIR’s Katharina Heil and Frederik Coppens. Left to right: Johan Gustafsson, Jeff Christiansen, Katharina Heil, Melissa Burke, Frederik Coppens, Christina Hall, Tiff Nelson, Ziad Al Bkhetan.

Thanks to the strong connections that have been established between ELIXIR (the European life science data infrastructure) and Australian BioCommons, a large group of research infrastructure specialists from Europe visited Australia over July and August. An ELIXIR travel grant gave the opportunity to deepen working relationships and connections between ELIXIR and the Australian BioCommons, to integrate Galaxy service innovations globally, and to enable new connections to be made. The group of 14 ELIXIR software developers, system administrators and service administrators, along with the ELIXIR Belgium Head of Node and Co-lead of the ELIXIR Galaxy Community, Frederik Coppens, and the ELIXIR Programme Manager Communities and Training, Katharina Heil, were hosted in Brisbane, Canberra and Melbourne. It's a wonderful example of why we were enthusiastic to extend our collaboration agreement to 2028.

There were many strategically important outcomes during the visit:

• Katharina and Frederik accompanied BioCommons to a meeting with NCRIS representatives at the Department of Education in Canberra, which resulted in the suggestion of a potential joint session to represent the ELIXIR-BioCommons collaboration agreement at the upcoming International Conference on Research Infrastructures (ICRI 2024)

• A visit to the National Computational Infrastructure by Katharina and Frederik led to discussions about ELIXIR’s possible involvement in Supercomputing Asia

• Sveinung Gundersen (ELIXIR Norway) presented FAIRtracks, a new RDA working group on FAIRification of genome sequence annotations, at the Galaxy Community Conference and International Congress of Genetics. Work to incorporate the Australian Apollo service as a use case for FAIRtracks is continuing

• BioCommons connected Katharina and Australian Research Data Commons’ (ARDC) Kathryn Unsworth to discuss the latest developments in Digital Research Skills Australasia (DReSA), based on ELIXIR’s TeSS (Training eSupport System)

• Katharina and Frederik presented the Using FAIR by design approaches to scale the uplift of FAIR Research Data Management practices in research ARDC webinar 

• Katharina was an invited guest at a careers-focused fireside chat hosted by COMBINE Australia, the student subcommittee of The Australian Bioinformatics And Computational Biology Society (ABACBS)

• Frederik met BioCommons’ Johan Gustafsson to continue discussing the future directions of WorkflowHub, as part of Johan’s ongoing position as joint product owner of WorkflowHub

• Katharina shared her knowledge on building active communities around research infrastructure in an interactive BioCommons hosted online meeting of local scientific community builders.

The larger group participated in the Galaxy Community Conference (GCC2023) and associated events lasting 2 weeks. As described previously, the Galaxy Australia team showcased the innovations to the Galaxy Platform that they are driving at GCC2023, and the ELIXIR group’s presence provided wonderful opportunities for in-depth sharing of technical learnings and best practices that will have a long lasting impact on the overall global Galaxy project.

Galaxy Australia’s leadership has been recognised with the invitation of Gareth Price to join the Galaxy Executive Board. Intensive planning and substantial improvements to the Galaxy ecosystem were accelerated by key ELIXIR team members extending their visit, made possible by the generosity of the Galaxy Executive Board member, Ross Lazarus, who accommodated them in Melbourne.

Snapshots of the ELIXIR team’s visit:

• Saskia Hiltemann co-delivered a presentation with Gareth Price (Galaxy Australia project lead) on Managing hands-on data analysis training with Galaxy

• Katharina and Frederik gave an ARDC hosted webinar on Bringing FAIR Research Data Management to Researchers at Scale

• Björn Grüning spoke at the BioCommons ‘BioChats’ meeting in August on Developing, deploying, and executing scientific data analyses in Galaxy and beyond.

Global biodata resources: crucial infrastructure underpinning biodiversity research

The importance of globally-connected infrastructure, its dependence on distributed resources, and its potential fragility will be addressed at next month’s conference on Biodiversity Information Standards TDWG 2023.

Biodata Infrastructure within Australia and Beyond: Landscapes and horizons will be co-presented by Chuck Cook from the Global Biodata Coalition, Kathryn Hall from the Australian Reference Genome Atlas, and Jeff Christiansen from the BioCommons.

This session will characterise the worldwide biodata infrastructure (Global Core Biodata Resources (GBC) and an inventory of biodata resources). Managers of data resources and aggregators are invited to discover the context of the entire infrastructure and to explore the scope and scale of connections and dependencies with other resources; the funding sources for the resources; and the impacts arising from the funding uncertainty associated with the underlying resources.

Life science data resources are numerous, distributed and variously interconnected, forming a singular, and arguably the largest, infrastructure for global biological research. These resources are critical for guaranteeing reproducibility and integrity for life sciences research, including biodiversity studies. Sustainably funding this disseminated infrastructure is a key challenge: the GBC is working with the funders who support many of these resources to ensure long-term funding for existing infrastructure, while also channelling support to underpin future growth in data volumes and new technologies.

TDWG 2023 is a hybrid conference taking place in Tasmania between Monday 9 Oct and Friday 13 Oct. In-person and virtual registration is now open.

Diverse range of BioCommons activities on display at eResearch Australasia 2023

The 2023 eResearch Australasia Conference will take place in Brisbane from 16 – 20 October. eResearch offers delegates interested in information-centric research capabilities the chance to engage, connect, and share their ideas. Sessions will cover how information and communication technologies help researchers to collaborate, collect, manage, share, process, analyse, store, find, understand and re-use information. 

A diverse range of BioCommons activities will be on show at the conference, presented by BioCommons staff and our collaborators. Please join us at the sessions below! 

Tue 17 Oct

10:05 am - Presentation: DReSA – a story of continuing collaboration in skills training (Melissa Burke)

10:25 am -  Presentation: Building Galaxy Labs to advance life science research (Gareth Price on behalf of Anna Syme)

2:15 pm - Birds of a Feather (BoF): Discussing the implementation of SciDir – A scientific software distribution repository for bringing reproducible software containers securely to HPCs in Australia (Greg D’Arcy - AARNet collaborator)

4:05 pm -  BoF: Driving community engagement with National Research Infrastructures (Melissa Burke)

Wed 18 Oct

11 am - Presentation: Curating species lists: Aggregating data to enhance context (Keeva Connolly speaking about the soon to be launched Australian Reference Genome Atlas, ARGA)

2 pm - Presentation: Visible & reusable workflows (Johan Gustafsson)

2:20 pm - BoF: Visible research software interest group (Johan Gustafsson)

4:10 pm - BoF: Putting Babel fish in our ears – creating a language for developers to talk to infrastructure designers and users for mutual gain (Mok, Keeva Connolly, Kathryn Hall - Atlas of Living Australia collaborator)

Thu 19 Oct

12 pm - Presentation: Knitting jumpers from steel wool and spaghetti: implementing a modified Darwin Core Event model for the Australian Reference Genome Atlas (ARGA) to increase trust through provenance (Kathryn Hall)

We look forward to catching up with many of you in person at the conference!

Register for eResearch 2023

Month-long visit of ELIXIR team to Australia

reposted from the ELIXIR EUROPE website

The ELIXIR team who travelled to Australia. Second left to right: Björn Grüning, Frederik Coppens, Paul De Geest, Katharina Heil, Helge Hecht, Laila Los, Helena Rasche, Saskia Hiltemann, Anthony Bretaudeau , Marie Josse, Krzysztof Poterlowicz, Katarzyna Kamieniecka and Alireza Heidari (missing, Wendy Bacon).

Over the (European) summer, a team of 14 ELIXIR experts visited Australia for a month to coincide with the Galaxy Community Conference (GCC2023), hosted by ELIXIR collaborators, the Australian BioCommons. The opportunity of GCC2023 brought Australian BioCommons partners, normally widely dispersed across the country, to a single location, and the presence of ELIXIR experts brought a European perspective to the global meeting.

On the technical level, the aims of the visit were to strengthen Galaxy system administration capacity in both Australia and Europe, share technical expertise to decrease the environmental impact of Galaxy, extend and improve the Galaxy training network, investigate the feasibility of running Pulsar as a global distributed compute network, and extend RO-Crate integration into Galaxy.

The strategic and scientific aims of the visit were to integrate biodiversity tools and workflows into Galaxy and the ELIXIR Research Software Ecosystem, align ELIXIR and European Open Science Cloud (EOSC) efforts (including EuroScienceGateway) with the plans of the Australian Biocommons, and deepen working relationships and connections between ELIXIR and the Australian BioCommons.

The ELIXIR team included software developers, system administrators and service administrators, along with the ELIXIR Belgium Head of Node (Frederik Coppens) and the ELIXIR Programme Manager Communities and Training (Katharina Heil). Funding was provided by the ELIXIR Travel Grant Scheme.

In addition to contributing to GCC2023, the ELIXIR representatives attended the Galaxy Community CoFest, ran three in-person Galaxy trainings for the Australasia community and visited Australian BioCommons partner institutions. The interactions enabled in-depth sharing of technical learnings and best practices, and provided an opportunity for strategic discussions on the newly renewed ELIXIR-Australian BioCommons collaboration agreement.

Katharina Heil and Frederik Coppens, as senior ELIXIR representatives, held discussions with representatives of the Australian Government’s National Collaborative Research Infrastructure Scheme (NCRIS), who fund Australian BioCommons. They also met with leaders from one of Australia’s two supercomputing centres, the National Computational Infrastructure (NCI), and featured in a webinar hosted by the Australian Research Data Commons (ARDC).

Björn Grüning, co-lead of ELIXIR Galaxy Community said:

“The sustainability of open source projects is dependent on collaborations and diverse contributions. Having the opportunity to work with the Australian Galaxy community across the continent has led to new ideas, projects and friendships that will have a long lasting impact on the overall global project. It's incredible how much we have learned from each other during the stay.”

Dr Gareth Price, Project Lead for the Australian BioCommons’ Galaxy Australia service commented:

“The long visit enabled fantastic exchanges between our team and ELIXIR international colleagues. Everyone is now energised and motivated to keep improving Galaxy Australia and strengthen our collaborations internationally.”

Collaboration boosts Galaxy services

Top left: Laila Los delivering the VueJS workshop. Top right: A short history of the Galaxy Training Network presented by Dr Saskia Hiltemann. Middle left and centre: Brainstorming sessions were held indoors… and outdoors. Middle right: Dolphin spotting! Bottom: Dr Saskia Hiltemann and Dr Gareth Price co-delivering the ‘Managing hands-on training with Galaxy’ webinar.

The global Galaxy family has capitalised on the rare opportunity to work in the same timezone, with key members of the Galaxy Europe team remaining in Australia after attending the Galaxy Community Conference. Thanks to a working visit sponsored by ELIXIR Europe, significant progress has been made to improve the Galaxy experience.

Dr Björn Grüning, Freiburg Galaxy team lead, welcomed the opportunity to work intensively with the QCIF and Melbourne Bioinformatics based teams:

“The chance to collaborate across all aspects of Galaxy in person has been extremely valuable. We’ve prioritised strategic discussions and sharing best practices over writing code, and now we have strong roadmaps for several projects planned out for the rest of 2023.”

Targets for development

The wide-ranging areas for development identified by these collaborative discussions will be rolled across Galaxy over the next 6 months - you can see the list of priorities on GitHub.

• User experience improvements including:

• A user-friendly workflow discovery page - directly inspired by Prof Carolyn Hogg’s GCC2023 keynote speech 

•  “Pinboards” offering quick and project-specific access to your favourite workflows, tools and training

• Direct plug-in of Galaxy Training to the user interface, offering recorded training sessions just one click away from tools or workflows

• Adding funding information to the metadata included with tools, allowing tool writers to acknowledge grants that support their work

• Optimisation and large dataset testing on Galaxy Australia of workflows from the Vertebrate Genomes Project, including one click imports to the Galaxy Australia Genome Lab. 

The team have found the simple act of working next to each other particularly helpful. Dr Anna Syme, Bioinformatician at Melbourne Bioinformatics and the Australian BioCommons, said that:

“The small day-to-day interactions that only happen in person have been a great chance to share our favourite tips and tricks when working with Galaxy. For example, Björn shared that user preferences can be set to re-use previous jobs rather than running them again, which has sped up the testing process of job-heavy workflows and saved me a lot of time!”

Presentations

During the visit, there have also been several formalised knowledge sharing sessions from both the Galaxy Europe and Galaxy Australia team.

• Managing hands-on data analysis training with Galaxy webinar by Galaxy Australia’s Dr Gareth Price and Galaxy Training leads Dr Saskia Hiltemann and Helena Rasche (both from Erasmus Medical Center, the Netherlands)

• A two day workshop on VueJS (the framework that Galaxy is built on) led by Laila Los, software engineer at The University of Freiburg

• Dr Björn Grüning discussed the semi-automated Planemo toolkit for developing, deploying and executing tools and workflows in Galaxy at the August BioChats meeting, and in a half-day, hands-on workshop at the Melbourne Bioinformatics office.

Keep a close eye on Galaxy Australia for improvements, and hear more about the upcoming developments by subscribing to the BioCommons newsletter.

Advice, infrastructure and support for community-scale bioinformatics training

The Australian BioCommons training team enables life science research excellence by creating opportunities to develop transferable skills in bioinformatics and to learn how to use new platforms, tools, services and techniques.

The team convenes the National Bioinformatics Training Cooperative and partners with the extended Australian BioCommons network to deliver practical and accessible bioinformatics training. We connect large organisations, small facilities, collaborative initiatives and individual experts to deliver community-scale training opportunities. 

Just as BioCommons forms partnerships to drive coordinated solutions to life science researchers’ problems, the training team supports specialists from our community to create training resources and events. We can support individuals and groups to share their specialist knowledge with the national community by:

• Implementing a framework for virtual or hybrid training

• Providing advice on training materials

• Taking care of event logistics

• Finding additional trainers to help with delivery

• Connecting with an engaged audience

• Choosing and accessing computational resources to support your training needs e.g. Galaxy Australia, Nectar Cloud. 

Read more about how we work in this case study of a successful training collaboration with researchers from the Genomics for Australian Plants consortium to deliver a series of high quality, live, hands-on learning opportunities.

Get in touch to find out how we can help bring your training to a national audience training@biocommons.org.au