ABLeS: Enabling Australian researchers to tackle challenges in bioinformatics

Dr Ziad Al Bkhetan presenting the three ABLeS allocation schemes.

The Australian BioCommons Leadership Share (ABLeS) has enabled 148 researchers from 26 institutes, organisations and research groups to respond to key bioinformatics challenges since its inception in 2021. Ahead of the upcoming webinar in March that will feature three participants from across Australia, we’ve spotlighted how some Australian life sciences researchers are leveraging ABLeS in their work.

The challenge

Researchers’ ability to leverage molecular analyses is continuously improving, and with this improvement come larger sample sizes, data sizes and computational complexity. This rapid expansion requires resource intensive analyses, plus the development of new, improved and optimised research software, particularly for reference data assets that require significant computational resources to prepare and maintain.

The Australian BioCommons response

The ABLeS program provides access to a mix of infrastructure and computational resources that has been specifically tailored to enable life science research groups to solve these challenges. The team behind ABLeS offers their extensive experience in research software engineering, digital infrastructure and bioinformatics to all participants, in the form of three distinct allocation schemes:

1. Reference data asset generation

Dedicated compute capacity is provided by ABLeS to allow efficient construction of reference data assets that are of enduring value to the research community, and will therefore underpin and enable downstream research. The Bioplatforms Australia Genomics for Australian Plants (GAP) framework initiative accesses this allocation type to advance our understanding of the evolutionary tree of life for flowering Australian plants, and to build complete plant genomes. GAP’s Bioinformatics Lead at the Royal Botanical Gardens of Victoria, Dr Theodore Allnut said:

GAP has produced vast amounts of sequence data that has required storage, processing, and analysis. Access to the supercomputer resources at NCI provided by ABLeS have been essential for GAP work. Overall, 17 botanists and bioinformaticians have processed their data on NCI’s ‘Gadi’ supercomputer and thanks to our ABLeS allocation, GAP has assembled 33 plant reference genomes, constructed the Australian Angiosperm Tree of Life, and undertaken six further species-level evolutionary studies.

2. Production bioinformatics

Research groups are supported to implement and run their existing best practice computational workflow approaches for omics data analysis at a much larger scale than is available through existing in-house computational infrastructure. This approach explains how ABLeS uplifted the research of University of Canberra’s Dr Ambikesh Jayal, Senior Lecturer in Data Science:

My team needed to extend our analysis to the whole Tasmanian Devil genome, which is fairly large (about 3 GB). Running such a large scale analysis was not possible in-house but the excellent and timely support provided by the ABLeS team means we are now running these analyses and plan to publish them in the coming months.

Dr Marie Wong-Erasmus, Principal Bioinformatics Engineer & Data Chair at the Children’s Cancer Institute said:

ABLeS first played a crucial role in creating high-quality and standardised reference datasets for The Zero Childhood Cancer program. Now, we are analysing these datasets using Pawsey infrastructure and we are constantly working to strengthen this partnership as our research program expands.

3. The Software Accelerator

The Software Accelerator supports the further development, installation, optimisation, testing and/or benchmarking of research software and focuses on a culture of software best practice. Bioinformaticians are supported to effectively implement, share, and document their work by embracing the FAIR (findable, accessible, interoperable and reusable) principles. Dr Cali Willet, Senior Research Bioinformatician at Sydney Informatics Hub, The University of Sydney, believes new opportunities have opened up with the ABLeS Software Accelerator:

ABLeS support has allowed us to optimise the highly popular DIA-NN proteomics tool for scalable high throughput analysis on HPC. We have tested and implemented this on NCI’s ‘Gadi’ supercomputer and are excited by the potential for proteomics studies to analyse thousands of samples at once within just one day of computing time.

All ABLeS groups are invited to contribute to, and benefit from, a shared repository of research software, housed by our partners at NCI. Dr Hardip Patel, Bioinformatics Lead in the National Centre for Indigenous Genomics at ANU and member of Bioplatforms Australia’s Australian Amphibian and Reptile Genomics (AusARG) Framework Initiative, sees great potential for the repository:

We've created a large-scale software repository for all the genomic resources prepared by AusARG by leveraging NCI resources under the ABLeS framework. We’ve utilised the repository to create analysis workflows, making them easily accessible to all NCI users and building Australia’s ability to initiate significant genomics projects.

Dr Ian Brennan, Postdoctoral Researcher at Australian National University and AusARG, described working with Ziad (BioCommons’ bioinformatics applications specialist) and the team as:

A fantastic, truly cross-disciplinary experience. The input and creativity of the BioCommons team has helped us to make our workflow much more efficient and user friendly, with the bonus of designing it to be lightweight and portable. Importantly, this means the workflow is no longer just a solution that works for our small research group - it can be picked up, used, and modified to suit a much broader community. Overall it has been a really satisfying and genuinely collaborative experience.

To learn more about the ABLeS program and hear directly from researchers involved, register now to attend the upcoming webinar on March 12.

ABLeS is co-funded by Bioplatforms Australia, National Computational Infrastructure and Pawsey Supercomputing Research Centre, and forms part of the national Australian BioCommons infrastructure.

Genomics in focus: Galaxy features at the 31st Plant & Animal Genome Conference

The international Galaxy Project recently participated in the 31st annual Plant & Animal Genome Conference (PAG31), the largest ag-genomics meeting in the world. The team hosted a hands-on workshop and offered presentations on next-generation sequencing data analysis, training, and the Vertebrate Genomes Project. Galaxy's dedication to open-source, FAIR data access, and comprehensive analyses shone through at PAG31.

Galaxy workshops leveraged the platform’s tools, workflows, and existing training materials. Workshop attendees experienced running their own microbiome analyses on reference data, and the assembly and annotation of microbial genomes. One workshop emphasised the integration of long and short-read sequencing methods and highlighted the significance of predicting protein structures using ColabFold, bridging genomic sequencing data with functional proteomics analysis. Participants agreed they had gained a deeper understanding of Galaxy's capabilities.

A spotlight on the Galaxy Training Network (GTN) emphasised its collaborative, open, and FAIR approach to scientific training materials. With over 300 tutorials authored and reviewed by a global community, the GTN serves researchers, educators, and scientific tool developers.

The Vertebrate Genomes Project (VGP) took the spotlight at PAG31, offering a series of talks that delved into the project's ambitious goal of generating phased, error-free, chromosome-level, near-complete, and annotated reference genome assemblies for all ~75,000 extant vertebrate species. Galaxy is a linchpin in the VGP's mission, facilitating seamless data integration, analysis, and collaboration among researchers. Galaxy is helping to overcome challenges related to genome-wide alignments, phylogenetic tree inference, universal gene nomenclature, and comparative genomics of specialised traits within the VGP's Phase 1 scientific studies, in which a representative species from (nearly) every vertebrate order will be assembled and released. Extensive documentation to guide users implementing the genome assembly workflows has been prepared by Dr Anna Syme, BioCommons bioinformatician and Galaxy Australia workflows specialist.

The recent paper ‘Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy’ identified how Galaxy is a crucial component in the VGP methodology and underscores Galaxy's pivotal role in enabling cutting-edge genomic studies on a global scale.

The ‘Justice, equity, diversity and inclusion’ workshop investigated how to acknowledge and address systemic injustices in genomics, and encourage and establish an environment where the field can realise its full scientific potential while embracing social responsibility and inclusivity. Prof Carolyn Hogg’s presentation, ‘Implementation: Genomic Resources’, highlighted the role Galaxy Australia plays in her work and emphasised the importance of integrating tools like Galaxy in the pursuit of justice, equity, diversity, and inclusion within genomics. Carolyn is co-lead of the Australasian Wildlife Genomics Group at the University of Sydney, Science Lead and Chair of the Bioplatforms Australia Threatened Species Initiative, and we are thrilled to see her regularly championing the use of the Galaxy Australia service by her genomics and genetics research peers.

This story was adapted from the detailed meeting report on the Galaxy Community Hub, where you can learn more about Galaxy’s involvement in PAG31.

Creative collisions: Bio Day a hit at Supercomputing Asia 2024

This month's Supercomputing Asia (SCA) conference featured a dedicated ‘Bio Day’ which focused on the intersection of biology and computing. Life scientists were enthusiastically invited to interact with the Asia Pacific high performance computing (HPC) community at the Sydney event. The conference organisers offered special access to almost 40 researchers and research infrastructure providers who were keen to participate in the biology-focused sessions. This extra support to add the unique voice of life scientists to the HPC forum was generously provided through Bioplatforms Australia's platinum sponsorship of the event.

Bio Day commenced with Prof Alex Brown, Director - National Centre for Indigenous Genomics, delivering a keynote presentation ‘Towards a National Indigenous genomics Ecosystem within Australia.’ As Professor of Indigenous Genomics at the Telethon Kids Institute and The Australian National University, Alex is an internationally leading Aboriginal clinician/researcher who has worked his entire career in Aboriginal health in the provision of public health services, infectious diseases and chronic disease care, health care policy and research.

Later, sessions titled ‘Building the Foundation: Genomic Data Infrastructure for Precision Medicine and Beyond’ showcased several key pieces of research infrastructure that Australian BioCommons has developed to support life scientists including:

• The Australian BioCommons Leadership Share (ABLeS)

• The Australian Alphafold Service

• The newly funded GUARDIANS project

• A pilot program bringing Seqera Platform to Australian researchers

Some of BioCommons’ significant national partners such as the Australian Amphibian and Reptile Genomics Initiative (AusARG) and international collaborators ELIXIR were also showcased on Bio Day. Additionally, Dr Kate Michie’s (UNSW) talk revealed the ‘Transformative Impact of Deep Learning on Accelerating Molecular Research: A Focus on AlphaFold2 and its Implementation Challenges.’ The Skills and Training Track on the same day also featured our training guru, Dr Melissa Burke, presenting our unique Training Cooperative model.

Sessions held on Bio Day illuminated the unique challenges that bioinformatics research brings to HPC, including:

• Episodic and extended access is required for compute resources

• Compute use is reliant on experimental outcomes, and difficult to predict in advance

• Software is diverse, rapidly evolving, and in many cases not optimised for HPC

• Researchers may have limited experience working in HPC environments

The light shone on these unique challenges stimulated some uncommon conversations at SCA, which aim to improve life science researchers' access to appropriate and scalable bioinformatics methods and compute resources. Dr Johan Gustafsson, Bioinformatics Engagement Officer at BioCommons said:

The conference was a unique opportunity to bring two worlds together - researchers working hard in their particular field of biology don’t normally attend HPC conferences, and vice versa. So it was great to see them starting to speak the same language!

Uwe Winter, BioCloud DevOps Engineer at BioCommons attended a workshop on the recently launched Trillion Parameter Consortium (TPC), a group formed to address the challenges of building large-scale artificial intelligence (AI) systems and advancing trustworthy and reliable AI for scientific research.

Discussions at the TPC workshop brought up a lot of exciting ideas on utilising AI in a fully automated research environment. I was inspired to hear TPC’s future plans and can’t wait to apply them to BioCommons infrastructure for the benefit of Australian researchers!

Overall, Bio Day at SCA was a fantastic chance to continue important conversations around the specialised support and infrastructure that life scientists need. BioCommons extends our thanks to Bioplatforms Australia for their sponsorship and to the conference organisers for running a successful event.

Galaxy Australia celebrates 8 million jobs to open 2024

University of Sydney researcher, Jess Hawes, recently demonstrated that Galaxy Australia is the platform of choice for many researchers conducting bioinformatics analyses. The team behind the service have been eagerly awaiting submission of the key 8 millionth job and were thrilled when Galaxy-newcomer, Jess, lodged a suite of jobs to support her fascinating PhD project.

Jess is part of Dr Alyson Ashe’s research group within the School of Life and Environmental Studies at the University of Sydney and has rapidly become a sophisticated user of Galaxy Australia who processes up to 300 Gb of sequence data at a time.

Prior to starting my PhD, I had never done any bioinformatics and the prospect of jumping straight into command-line was intimidating. My supervisor suggested I try Galaxy Australia first. The setup was so quick, there were heaps of guides, templates and shared workflows that I could use to start from, and there’s a massive global community with lots of support and tips. It has been a really good introduction to bioinformatics!

Jess is working to understand the molecular basis for epigenetic inheritance, using model organism C. elegans to investigate how histone modifications and small RNAs interact in the context of epigenetic inheritance. Her workflow is completed end-to-end without leaving the Galaxy Australia site: from preparing sequencing files, pairing them, trimming off the adapters, aligning the reads to a reference genome and calling peaks. With large amounts of data to process at once, Jess requested extra storage:

It was so easy to ask for extra storage and I had a response within days. The email from the team saying that I’d be able to access 2 TB was such a relief! And for free!

Jess finds the Galaxy web interface very user-friendly:

I love that it saves a lot of the parameters and inputs that lead to the generation of different files. This means I can easily work out which inputs and which variables lead me down the right path. I also love that within Galaxy, if one of my samples fails at step 3 of 10 in the workflow, all the future steps that rely on that sample pause. This means I can go back, find the step that failed, troubleshoot and then re-run that one sample. There’s even a little toggle option that means after this step successfully runs, all the following steps will also resume. This means I am not stuck repeating every single step every time for all my datasets when only one step fails – saving both my time and computing time!

Overall, Jess has improved a wide range of skills through her experience using Galaxy Australia, describing it as:

A really good introduction to working in a command-line setting. If I needed to, I’d be more confident jumping into the back-end side of things. But so far I haven’t needed to because everything is ready to go!

Jess is one of more than 30,000 researchers who have used Galaxy Australia in their work. If you haven’t already, head to usegalaxy.org.au to get started today!

Streamlining metagenomics and single cell transcriptomics data processing with new workflows

Three new computational workflows are transforming raw metagenomics and single cell transcriptomics data into an analysis-ready state. Perfect for fresh experimental data or analysis of publicly available datasets, the workflows come with best practice tools installed and well documented how-to guides. While originally developed for use by a core facility generating huge quantities of new data, the new resources are available on the fully subsidised Galaxy Australia service so that anyone can put them to work. 

The workflows were developed through a collaboration between Griffith University’s Central Facility for Genomics (GU-CFG) and Australian BioCommons. With an expected influx of spatial omics and single cell data from new instrument installations, these common workflows were the ideal solution to do the heavy lifting of data preprocessing before delivery to end users.

Dr Sarah Williams, Senior Bioinformatician at QCIF, said that the team built their workflows within the Galaxy Australia platform as:

“The web accessible interface is intuitive to use. Histories can be quickly shared along with custom reports for GU-CFG to provide to their end users, and researchers can then choose to continue with further analyses without leaving the Galaxy interface.” 

Valentine Murigneux, Bioinformatician at QCIF added:

“Researchers can just bring their data into Galaxy and use the workflows straight away, as they come with the best practice tools pre-selected and installed ready to go on Galaxy, saving time often spent researching the best tools for the job and installing the databases required.”

One example of this benefit is the inclusion of CellRanger within the single cell RNA (scRNA) sequencing workflow. CellRanger is a proprietary tool for 10X single cell data, and access is now fully subsidised for Australian-based researchers through an application process within Galaxy Australia.

All three workflows have extensive user guides available, so if you are looking to efficiently process raw metagenomics or single cell transcriptomics data, be sure to check out the new workflows via WorkflowHub:

• scRNA sequencing

• Shotgun metagenomics

• 16S metagenomics

You’ll find all of the background information you need about the workflows in their how-to guides:

• scRNA sequencing

• Shotgun metagenomics

• 16S metagenomics

Looking ahead, BioCommons are establishing two new activities - the ‘Methods Commons’ and ‘BioCLI’ to continue where BYOD has left off. Stay tuned for more in this space!

Read a full summary of the BYOD Expansion project

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The Australian BioCommons BYOD Expansion Project was funded through NCRIS investments from Bioplatforms Australia and the Australian Research Data Commons (https://doi.org/10.47486/PL105) that were matched with co-investments from AARNet, Melbourne Bioinformatics, NCI, Pawsey, QCIF via the Queensland Government RICF fund, The University of Sydney, AGRF, Griffith University and Monash University.

Partnership with Genetics Society of AustralAsia enables quality new training

A novel training opportunity is available thanks to a collaboration between the University of Auckland’s Dr Katarina Stuart, the Genetics Society of AustralAsia (GSA) and Australian BioCommons. The genetic outlier analysis workshop will introduce participants to the basics of genomic selection analysis. Delivered online across 27-28 Feb 2024, the code-along sessions will step through the process of identifying signals of selection using the outlier analysis method in an example genomic dataset. 

Lead trainer Katarina’s previous research has involved an array of genomics approaches to explore rapid adaptation in the invasive bird, the European starling, and her current postdoctoral research investigates the role of transposable elements in other biological invasions. Seeing that others could benefit from her experience in the area, Katarina initially developed the workshop with financial support from GSA and the Australasian Evolution Society, which led to in-person workshops in Aotearoa/New Zealand. Demand for that workshop led to a collaboration with BioCommons to facilitate a virtual version and an invitation to offer the valuable training in Australia.

A new partnership with GSA and BioCommons is enabling this busy researcher to deliver her high quality training workshop internationally. A broad range of researchers have already applied to take part in this unique opportunity, which will for the first time be underpinned by the BioImage environment on the powerful Pawsey Nimbus Research Cloud.

Do you want to participate in the workshop?

This workshop is for members of the Genetics Society of AustralAsia and/or researchers associated with an Australian research organisation who will use genomic selection analysis as part of their projects. The workshop is free but participation is subject to application with selection. If you are interested, read through the details and apply by 9 Feb 2024.

Further in-person workshops will be offered later in 2024. These will be designed for researchers who already have their own data, so that participants can begin applying these techniques to their own datasets, and comparing outcomes with other participants.  

Do you have training materials that your peers could learn from?

GSA offers an ongoing Workshop Support Program that provides contributions towards workshops that share knowledge and/or exchange ideas across genetics. Up to $1,000 AUD funding can be provided for up to 5 events per year on a competitive basis. There is an easy application process and the call outs for proposals generally close in June each year.

BioCommons can offer support for training events in lots of ways - from providing the compute environment you need to connecting you with the right participants. We partner with professional associations like GSA to ensure we are supporting the training that the research community needs.

Wrapping up the ‘Bring Your Own Data’ project and a look to the future

Important Outputs

• Australian Apollo Service
• Australian Alphafold Service
• Australian Fgenesh++ Service
• Grew Galaxy Australia significantly, from two to seven million submitted jobs
• Established Galaxy Australia’s TIaaS and the Genome Lab
• Tool Finder
• Seqera Platform pilot
• Bioimage, a purpose built bioinformatics environment on the command-line

Four new national services, major expansions to Galaxy Australia, 15 training workshops and webinars, many specialised workflows, and even more stories of impact, all thanks to collaborative efforts of 12 organisations. It’s fair to say that the Australian BioCommons ‘Bring Your Own Data’ (BYOD) project met its aim to enable highly accessible, available, and scalable data analysis and sharing capabilities for the benefit of Australian life science researchers.

Winding down at the end of 2023, the BYOD Expansion project’s legacy will continue through the delivery and constant improvement of our national services. 

The project began in June 2019 thanks to investment from BioPlatforms Australia and the Australian Research Data Commons (ARDC), and brought together a large group of collaborators and co-investors including AAF, AARNet, Melbourne Bioinformatics, NCI, Pawsey, QCIF via the Queensland Government RICF fund, The University of Sydney, AGRF, Griffith University and Monash University. There were three focus areas: web-based bioinformatics workbenches for life sciences researchers, a complementary command line interface (CLI)-focused platform, and creation of data infrastructure connecting ‘omics instruments and reference datasets to the analysis infrastructure. Work in these areas has had a wide ranging and extremely positive impact on the life sciences research landscape, as showcased in the words of infrastructure end users.

TESTIMONIALS

Tool Finder will be a really useful resource for researchers, particularly those who are just getting started and want to understand what software is available for their analysis and what computing platform would be most suitable. It’s awesome to have all of that information on hand in the one place! 

Dr Parice Brandies, The University of Sydney

Galaxy Australia 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.

Dr Kylie Munyard, Curtin Medical School

The Fgenesh++ service has helped us easily and efficiently annotate multiple diverse genomes to a high standard.

Dr Kate Farquharson, The University of Sydney

For my PhD project I assembled close to 4000 RNA-Seq datasets from samples from all over the world - a task that would have been impossible without Galaxy Australia.

Dr Rhys Parry, University of Queensland

So much software gets left without regular updates and from year to year you realise that it isn’t maintained or updated. So we look for things that are stable - this is the reason we call on the Australian Apollo Service.

Assoc Prof Charles Robin, University of Melbourne

We are looking at how a particular genus of plant viruses evolved to only infect plants. We make virus-like particles in order to determine the structure of viruses and also for drug discovery and biomedical use. AlphaFold was used to check for evidence of a core structural domain of a putative coat protein and the fact that it was there gave us the confidence to go on and make virus-like particles.

Dr Frank Sainsbury, Griffith Institute for Drug Discovery

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, Australian BioCommons

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.

Alexandra Boyling, ANZAC Research Institute

Looking ahead, BioCommons are establishing two new activities - the ‘Workflow Commons’ and ‘BioCLI’ to continue where BYOD has left off. Stay tuned for more in this space!

Read a full summary of the BYOD Expansion project

---

The Australian BioCommons BYOD Expansion Project is funded through NCRIS investments from Bioplatforms Australia and the Australian Research Data Commons (http://doi.org/10.47486/PL105) that are matched with co-investments from AARNet, Melbourne Bioinformatics, NCI, Pawsey, QCIF via the Queensland Government RICF fund, The University of Sydney, AGRF, Griffith University and Monash University.

Australian satellite of BioHackathon Europe 2023 underscores the universal language of scientific collaboration

The Outpost team consisted of Cameron Hyde (QCIF, University of the Sunshine Coast), Igor Makunin (QCIF, University of Queensland / Australian BioCommons), Anna Syme (Melbourne Bioinformatics / Australian BioCommons), Michael Charleston (University of Tasmania), Locedie Mansueto (Southern Cross University), Johan Gustafsson (Australian BioCommons), Mike Thang (QCIF, University of Queensland / Australian BioCommons), Tom Harrop (Melbourne Bioinformatics / Australian BioCommons), and Siyuan Wang (Symbio Laboratories).

To bridge the geographical gap, an Australian team participated in an innovative collaboration to once again join BioHackathon Europe remotely. Providing a powerful opportunity for Australian contributors to shape global bioinformatics advancements, this fun annual ELIXIR Europe - Australian Outpost also offers a welcoming platform for networking with local and international peers.  

From 30 Oct to 3 Nov, a diverse team from around Australia converged on a Brisbane hotel, turning the apartment into a hub of innovative coding challenges. Ten people worked 2:30 pm - 12:30 am each day, while connecting live with the rest of the teams in Barcelona and online. The highly anticipated annual event saw 350 participants from around the world come together to work on 35 projects. 

Reflecting the rich multicultural fabric of Australia and the global nature of the event, the team showcased a remarkable diversity of backgrounds. Composed of individuals born in England, China, the Soviet Union, the Philippines, Malaysia, New Zealand, and Australia, and ranging from postgraduate students to seasoned professors, our team brought together a tapestry of experiences, perspectives, and expertise.  We welcomed familiar faces and newcomers who responded to our public call for interest, and participants from both academia and industry. They brought interests in mathematics, biology, computing and bioinformatics and exchanged more than a few skills along the way.

Our group mirrored the inclusive spirit of the BioHackathon, working hard into the night to contribute to one or two of our chosen projects:

• Galaxy ENA Upload as an Interactive Tool

  A big leap forward was made to the process to interactively build the metadata required for successful ENA data submission. This team worked on a new interactive Galaxy tool that allows a researcher to pick and populate one of 30+ ENA templates, and re-focused the ENA upload tool in Galaxy to accept only prepared ENA templates.

• Genome annotation and other post-assembly workflows for the tree of life

  This team contributed to a broad examination of analysis pipelines by running annotations for several species using multiple Galaxy tools. The results have kicked off ongoing work to consolidate tools and relevant settings into user-friendly workflows.

• Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific Communities

  The project created an interactive table prototype that increases the findability of the Galaxy microbiome analysis tools, and which can now be reused by other Galaxy domain communities. The process of updating bio.tools registry entries and linking each Galaxy tool to these entries was started, and will ensure the completeness of the table metadata over time.

Aside from the progress made on each of the projects, the Outpost provided the opportunity to “meet new people and continue building working relationships with international colleagues” which has already resulted in “multiple collaborative outcomes from the projects” according to Dr Johan Gustafsson, BioCommons’ Bioinformatics Engagement Officer. Siyuan Wang, from Symbio Laboratories, said: “The Outpost was a perfect opportunity to meet new people in a similar field and I got to work on exciting projects that I wouldn’t normally have had a chance to do.” From the European side, Dr Nicola Soranzo, who currently works at the Earlham Institute as Galaxy Platform Development Officer found the virtual connection worked very well, and was thankful for a “great collaboration with the Aussie Outpost!”

ELIXIR generously supported the in-person attendance of Dr Gareth Price from QCIF. As Galaxy Australia’s Lead, Gareth was well placed to act as our Barecelona connection point. He helped to raise awareness of our Outpost and facilitate discussions and presentations on behalf of the Aussies. We are extremely grateful to ELIXIR for working with us in the lead up to the event to make sure our contributions were optimised.

We’ll bring together a new team for the next BioHackathon Europe in Nov 2024 - maybe you will join us next time!

New online tutorials embed genomics into conservation management decisions

Photo credits: Left Kate Quigley, centre Nick Bradsworth, right Carolyn Hogg.

A new online course is available that promises to increase the use of genetic data in Australian conservation management actions. Developed by the Threatened Species Initiative (TSI) and the University of Sydney in collaboration with some of Australia’s leading conservation geneticists, the tutorials have been made freely available to everyone via the Australian BioCommons YouTube Channel.

Genetics and genomics are powerful tools for understanding global biodiversity, with a wide range of applications for policy, ecology, translocations, evolutionary biology and more. The Conservation Genomics for Threatened Species Management course was developed by TSI, which brings a network of researchers into direct contact with conservation agencies and policy makers, enabling research outcomes to directly influence on the ground conservation decisions. As one of Bioplatforms Australia’s key Framework Initiatives, TSI reached out to BioCommons for support to edit and host their community’s content.  Prof Carolyn Hogg, Senior Research Manager, Australasian Wildlife Genomics Group at the University of Sydney, and Science Lead and Chair of TSI, brought together a panel of field experts to explain how cutting-edge genomics technologies, genetic tools and advanced computational biology can assist and guide conservation management strategies.

The inaugural @ThreatenedSpGen workshop on using genetics for conservation management was a hit! A great group of people from all over, really engaged in upskilling their genetic literacy. #ictc23 @ellemclennan @persoonia @BioplatformsAus @Sydney_Science @Science_DBCA pic.twitter.com/zumixBBW1p

— Prof Carolyn Hogg (@HoggCarolyn) November 12, 2023

The ten modules can be viewed independently, and the course materials have already been used at a workshop during the 2023 International Conservation Translocation Conference. The suite of videos will be added to over time, but so far feature speakers from the University of Sydney, Monash University, University of Adelaide, Australian National University, Minderoo Foundation, Arthur Rylah Institute for Environmental Research, Research Centre for Ecosystem Resilience at the Botanic Gardens Sydney, Taronga Conservation Society Australia, NSW Government Savings our Species program, and the Government of Western Australia Department of Environment and Conservation. 

You can learn more from Carolyn about how TSI is bridging the gap between genomicists, bioinformaticians, conservation experts and decision makers to help save Australian species by visiting the refreshed TSI website. Or watch her BioCommons webinar ‘Conservation genomics in the Age of Extinction’, to learn more about using cutting-edge genomics technology and advanced computational biology to assist in conservation management for species recovery.

View the Conservation Genomics for Threatened Species Management playlist

User experience insights help design better services for researchers

A key question is right there in the URL usegalaxy.org.au: How do you use Galaxy Australia? Australian BioCommons User Experience Designer, Mok, recently analysed the journeys that users take when accessing the Galaxy Australia service. Mok’s research has provided a clear direction for improvement that has been taken up by the international Galaxy project. Simple, fundamental changes are planned based on how you use Galaxy.

The Galaxy Australia team’s commitment to constantly improving the service required insight into the many different ways that researchers use Galaxy. Mok worked with Galaxy Australia’s user experience designer, Madeline Bassetti to examine the experiences of Australian users.

Mok’s findings provide a visual story of how researchers interact with Galaxy Australia, including developing personas for different types of users including bioinformaticians, e-research analysts and PhD students. Each persona has distinct characteristics (eg. their familiarity with using Galaxy), allowing the Galaxy team to further analyse user experience within the appropriate context and prioritise which new features and improvements to implement first.

Interactions with Galaxy Australia were investigated according to the stages of plan, collect, process, analyse, preserve, share and reuse, as described in the ELIXIR RDMkit data lifecycle.  Many users begin their journey at the analysis stage, however Mok’s research identified that Galaxy Australia has an important role to play at each lifecycle stage. By documenting users’ pain points, Mok identified opportunities and recommendations to improve Galaxy Australia across the whole data lifecycle. After a recent presentation at the Galaxy Community Conference, the international gathering of Galaxy developers shared that they “found the talk super helpful, particularly the user journey maps,” and noted that “this work is a huge time saver for the rest of the [international] Galaxy project.”

As a result, Mok was invited to present a full report at one of the Galaxy Community Calls, where US, EU and Australian Galaxy development teams gather to share updates and discuss improvements to the Galaxy. An international team has formed to combine Mok’s work with website analytics to gain further insights. Ultimately, this user journey research will inform future improvements to the entire Galaxy ecosystem.

Go ahead and look at the latest updates, start your own journey to use Galaxy, or if you have a deeper interest, consider joining a Galaxy Community Call in the future - everyone is welcome!