Participating in the nf-core Hackathon 2025: the Sydney satellite
Magda shares her experience at the Australian outpost of the international hackathon!
BY Magda Antczak, bioinformatician, qut & QCIF LTD
The nf-core hackathon was such a great mix - it offered something for everyone, whether you're a seasoned Nextflow user or just starting out with pipeline coding like me.
Working together in the same room was amazing, especially since so much of our work happens online nowadays. I finally got to meet people in person who I'd only known on Zoom before, and we collaborated on projects together.
Everyone was so helpful, and we even managed to sit down and figure out how to use nf-test to test pipelines—a task we'd been putting off because it seemed overwhelming. It turns out that it's intuitive and not as scary as we thought. We have even written some test cases for our pipelines!
On top of the productive work, the event was so well-organised. The room was comfy, the lunch was delicious, and we had snacks and coffee on hand whenever we needed. A big shoutout to Giorgia for her coffee runs and for looking after me like a mum when I wasn't feeling well. All in all, it was a wonderful mix of learning, collaboration, and camaraderie.
If Magda’s experience has got you interested in the Aussie outpost of the hackathon, you can read BioCommons short report on the event here.
Information about the international event is here.
Subscribe to the Australian BioCommons newsletter to make sure you hear about events like this!
Three practical resources to boost your training skills
Thinking about upskilling as a trainer but not sure where to start? Here, I share my experience as a trainer (and former researcher!) with three great Train-the-Trainer resources - what they offer, how they differ, and which one might be the best fit for you, depending on your goals.
By Giorgia Mori, BioCloud Training and Communication Officer, Australian BioCommons
As a researcher turned trainer, I know firsthand how challenging it can be to learn how to improve the way you teach. In my own journey towards becoming a professional trainer, I’ve taken many courses - some better than others! We thought it would be useful to compile a list of opportunities to help aspiring trainers to teach effectively and ensure that learners walk away feeling their time was well spent.
The Skills for Trainers Collection, curated and endorsed by Australian BioCommons, is full of resources to help you boost your training skills. As you explore the resources in this collection, you may wonder which one is best suited to your needs. Below, I share my insights on how three of these excellent resources can be particularly useful depending on your goals as a trainer. I hope these notes will help you navigate the options and make informed choices.
Flowchart comparing Train the Trainer courses: The Carpentries, Teaching Tech Together, and Future Learn. The chart is divided into three sections: Learning, Design, and Teaching. Each section lists characteristics shared by the courses or specific to one or more of them.
Lessons from The Carpentries: building confidence through live interaction
Format
Sign up via The Carpentries website and complete a short application process. The training consists of 16 hours of interactive online or in-person sessions (typically over two full days or spread across multiple shorter sessions). Participants must complete pre-workshop reading, actively engage in discussions and exercises, and submit a short practice teaching demonstration. Fees vary depending on whether you attend through a partnered institution, an open enrolment session, or apply for a scholarship.
Best for
Developing confidence in live-coding as a teaching method and creating an engaging, interactive learning experience for learners.
The Carpentries Instructor Training provides a strong foundation for teaching programming skills, with a focus on live coding as the primary method of delivery. This technique role-models instructors solving problems and writing code in real time, offering learners an authentic, transparent experience. It’s an approach that fosters engagement and builds confidence, as learners see mistakes and debugging as natural parts of the process.
One of the most valuable aspects of this training is its emphasis on creating inclusive learning environments. Techniques such as setting expectations, encouraging questions, and normalising mistakes are essential for ensuring that all learners feel comfortable and supported.
Additionally, the focus on practical teaching tools, such as formative assessments, concept maps, and learner personas, provides trainers with methods to tailor their instruction to different audiences. These techniques are particularly useful in engaging participants with varying levels of experience.
FutureLearn Train the Trainer: designing for outcomes and sustainability
Format
Enroll through the FutureLearn platform. The course is self-paced and available on demand, allowing participants to start and finish at any time. It typically runs for 3–4 weeks with a suggested commitment of 3–5 hours per week. The course is free and includes video lectures, readings, discussions, and reflective exercises. To obtain a certificate, participants must complete all course activities and pass a final quiz.
Best for
Focusing on designing effective training sessions, structuring learning experiences for maximum impact rather than just delivering content.
The FutureLearn Train the Trainer program offers a more design-oriented perspective, making it an excellent complement to other resources that focus on delivery. A standout feature of this course is its structured approach to training design, particularly the use of backward design. Starting with the learning outcomes and working backward to align activities and assessments ensures that sessions are focused and purposeful. This is especially valuable in the bioinformatics field, where time and resources are often limited.
Another highlight is the course’s exploration of teaching styles and barriers to learning. By encouraging trainers to reflect on their own approach and recognize challenges learners might face, the program fosters a deeper understanding of how to create effective and inclusive training environments.
Discussions around group dynamics and facilitation techniques are also particularly relevant for workshops, where managing interaction and engagement can significantly impact learning outcomes.
If you are not interested in full certification but still want to improve your skills, this training allows flexibility to skip sections and focus on key takeaways such as goal-setting, resource planning, and facilitation strategies.
Teaching Tech Together: a practical toolbox
Format
The book is freely available online as an open-access resource (in English and Spanish language) and can also be purchased in print. Readers can engage with the content at their own pace, exploring topics as needed. There is no formal completion process or certification. You can use the book as a reference, working through exercises and activities independently or incorporating them into your teaching practice. Sections can be skipped or revisited based on individual needs.
Best for
Investigating an accessible and flexible approach to improving training skills. Ideal if you prefer a practical, action-oriented learning style.
This is a compact yet rich resource that offers trainers practical guidance for teaching technical skills. What sets this book apart is its abundance of exercises and activities, making it an excellent starting point for anyone looking to build ad-hoc Train-the-Trainer programs or facilitate team-building sessions.
The exercises are designed to be immediately actionable, helping you introduce formative assessments, set clear learning objectives, and engage learners effectively. These activities are adaptable and can be tailored to suit different audiences.
While the book doesn’t delve into content design or evaluation in depth, its value lies in its practicality. It provides you with tools you can pick up and use without needing to commit to extensive pedagogical training.
Conclusion: choosing the right resource for your training journey
The resources I’ve explored each offer unique strengths. If you’re looking to improve confidence in live teaching, The Carpentries is a great starting point. If your focus is on structuring training for impact, FutureLearn’s design-oriented approach is invaluable. They also give you the opportunity to obtain a certification. Both courses, however, require practice and preparation to fully master their approaches. Meanwhile, Teaching Tech Together offers an abundance of practical exercises to reinforce these skills and engage trainers in hands-on learning. Both FutureLearn and Teaching Tech Together resources have a section about online teaching. With practical tips on maintaining attention and fostering interaction in virtual environments, these addresses challenges that many trainers face in today’s hybrid learning landscape.
The choice of resource depends on your goals.
You can also mix and match the best strategies from each. Think of it like crafting the ultimate training recipe; blend live coding confidence from The Carpentries, FutureLearn’s structured design, and Teaching Tech Together’s hands-on activities to create engaging, effective learning experiences. The best trainers are always learning, so why not take a little inspiration from all three?
We’d love to hear what resources have helped you build your training skills!
Share your favorite books, courses, or tools with us through email at training@biocommons.org.au
List of resources:
The Aussie Outpost of BioHackathon 2024 was a blast! Here's why:
George shares his fantastic experience at BioHackathon 2024!
BY George he, Master of Genomics and Health student, The University of Melbourne
Allow me to set the scene for one of the most exciting events I attended to this year:
ELIXIR's 2024 BioHackathon: Aussie Outpost
Destination? Brisbane, in one of the city centre’s most defining towers, overlooking an expansive landscape and its glorious river network.
Twenty hackers from around the nation converged here, bringing a wealth of experience in bioinformatics, life sciences, and software engineering to collaborate on projects tackling critical challenges in the bioinformatics world. Many of the projects focused on enhancing data integrity, interoperability, and usability, developing better practices for research and data sharing.
As for me? I was grateful for the chance to participate, to meet and work with established professionals in their fields, and, I must say, we had a terrific time. I had only entered the world of programming last year during my Master’s degree and had recently completed a subject on database systems and information modelling. But, one of the definitive moments of the hackathon for me was moving between projects and quickly adjusting to the new one. What I thought would take me all night to grasp, I picked up in just five minutes! My studies and experiences had placed me in the perfect position to dive into the project quickly. All the knowledge I’d gained over the year came flooding out for me to apply.
You might be wondering at this point, what exactly did we achieve at this BioHackathon?
Of the three projects the outpost was collaborating on (Project 31: Executable Metadata Mappings to FAIRify Biodiversity Genome Annotations, Project 11: Galaxy CoDex, and Project 8: Data Model Converter), I was fortunate enough to move between Project 11 and Project 8. By doing so, I absorbed so much knowledge about the Galaxy platform while applying the programming and database modelling skills I had been developing. It was also a general pleasure, and a unique experience, to watch a multifaceted team come together, communicate, and collaborate with our international counterparts.
Galaxy CoDex focused on ensuring the future sustainability of the well-established open-source Galaxy platform for data analysis. As a continuing project from the previous year, I had the guidance of Gareth and Mike, who are both highly respected in the Galaxy community. They patiently brought me up to speed on the use of Galaxy and its benefits for data analysis. The project centred on helping users find the right tools to analyse their data and improve workflows by adding appropriate metadata to the underlying code. Instead of manually searching through thousands of tools available on the platform, metadata annotations would improve tool suggestions and allow custom workflows to be created automatically. This would increase the searchability and usability of Galaxy tools. I learnt a great deal about the Galaxy Project platform, the importance of metadata and tool annotation best practices, and brushed up on my GitHub skills, even contributing small updates to the project.
Josh and Christian presenting the Data Model Converter to the rest of the group.
In Data Model Converter, our team created a functional web application to convert between two clinical data models (FHIR and OMOP), becoming a valuable tool for transferring patient data or supporting research across hospitals. I was impressed with how quickly I onboarded this project, as it was a practical application of my studies this year. On one hand, I had experience with creating custom Python classes during my data analysis internship; on the other, my knowledge of database systems and information modelling. Combining these experiences, I quickly integrated into the team and figured out how my skills could best meet their needs. I contributed by helping the team test the data converter’s robustness and drawing data modelling diagrams to help users understand how the converter worked. It was so rewarding to apply what I had previously learned in theory and assignments. This wouldn’t have been possible without the unique skills and experiences I’d gained over the year. How good’s that?
This BioHackathon was a BLAST. It felt fantastic to be involved in the bioinformatics community, to learn from and collaborate with like-minded individuals. I’m excited to see how these projects shape the bioinformatics community and look forward to participating in future BioHackathons, to meet even more people in Australia and beyond!
If George’s experience has got you excited for future BioHackathons, subscribe to the Australian BioCommons newsletter to make sure you hear about the next one!
GCC2024 celebrates Galaxy Australia contributions
Gareth reflects on the 2024 Galaxy Community Conference and celebrates how frequently the Galaxy Australia team were cited as important contributors to global initiatives
BY DR Gareth Price, Project Lead of Galaxy Australia
The 2024 Galaxy Community Conference was held in Brno, Czech Republic - a city best associated with Gregor Mendel’s contributions to our understanding of heredity. I was lucky enough to attend in person, along with Catherine Bromhead - Lead of Galaxy Australia’s Infrastructure team - thanks to Australian BioCommons funding. At the event, I was extremely proud of how frequently the Galaxy Australia team were cited as important contributors to global initiatives!
Catherine delivered a presentation - Metascheduling with TPV: Weighting jobs on multiple constraints for distributed deployment over local and remote resources - that described her work with Justin Lee and Nuwan Goonasekera. Her talk was enthusiastically received, with Galaxy Admins from around the globe quick to ask if the work can be adopted for use on their services - for which the answer is a firm yes! This work builds on Galaxy Australia’s previous open-science contribution of TPV by now providing further nuanced control of job scheduling, which benefits users by maximising the number of concurrent jobs they can run.
Catherine was also among the founding participants of Galaxy VENUS, a meeting of the women and non-binary members of the Galaxy community, which promises to become a staple at future GCCs. Launched by Wendi Bacon, Natalie Kucher, Bérénice Batut, Helena Rasche, and Saskia Hiltemann, it’s fantastic to see diversity as a key focus for the Galaxy community.
It was great to see the Galaxy Australia team receiving numerous ‘shout-outs’ during presentations and on posters, including:
My snapshots of the Galaxy Australia team’s shoutouts
Nuwan for his work on Galaxy’s password vault, and his contributions to estimating cloud computing costs when running bioinformatics workloads - stay tuned for a publication soon!
Anna Syme for her contributions to globally recognised high-quality and robust workflows, as issued by Galaxy’s Intergalactic Workflow Commission.
Anna and the entire Aussie Outpost of ELIXIR’s BioHackathon 2023 were pointed out as key contributors to new community-driven standards development for reference genome generation.
Johan Gustafsson (Australian BioCommons) received mentions for his work on the Galaxy Tool Metadata Extractor plus efforts to link Galaxy Australia workflows with WorkflowHub.
Cameron Hyde and Grace Hall for their pioneering work on Alphafold 2 for Galaxy
Cameron again for wrapping the interactive tool CellxGene, which is used in a set of reproducible single cell RNA-seq analysis pipelines for understanding early persister cells in cancer.
On a personal note, I was appreciative to receive a mention for participation in SPOC - the Single cell and sPatial Omics Community of practice. I also enjoyed presenting the achievements and plans for Galaxy Australia, as part of the annual State of the Galaxy talk, given by the leads of the major usegalaxy.* services. This was on the back of representing our national service at the important pre-conference satellite meeting, the Galaxy Directions Summit. The Summit galvanised an action I was keen to advance, which I did alongside Natalie Kurcher from John Hopkins University, to reboot the Galaxy Project Roadmap through open solicitation of ideas to be captured in the 2024 - 2026 vision for Galaxy.
GCC always ends on a high note with CoFest - two full days for all the excitement, energy and new learnings of GCC to be poured into the Galaxy code! Attending in person meant Catherine and I could get stuck in and make some big collaborative advances. Catherine worked on critical dependency refreshes for Galaxy, namely Python 3.13 and NumPy 2, while I worked with Wendi Bacon on the global unification of Galaxy Labs - read the recent Galaxy publication for more details. At CoFest, the Galaxy Lab style created in Australia by Cameron Hyde was adopted for global use, with the Single Cell Galaxy Lab migrated from Galaxy Europe into the global codebase. This work will continue at this year’s BioHackathon, including at the Australian Outpost.
As with each Galaxy Community Conference when it wraps up, I’m filled with energy to keep delivering Galaxy as a high-quality service to Australian researchers. Part of this excitement comes from knowing when we, the Galaxy community, will all get together again. It was tough to keep under wraps like we were asked, but as I write I’m now again excited about GCC2025, hosted in Cold Spring Harbour with the BioConductor community and celebrating Galaxy Projects 20th year. Find out more in the announcement.
And finally, a few pictures from around Brno!
Reflections on the successes of a national genomics consortium
Johan has supported GAP for over four years and shares his reflections on the journey.
BY DR JOHAN GUSTAFSSON, AUSTRALIAN BIOCOMMONS
The Bioplatforms Australia Genomics for Australian Plants (GAP) Framework Initiative recently published a preprint of the capstone paper for the consortium. I have helped to support GAP for more than four years as part of Australian BioCommons, and so this publication has led me to reflect on the journey. Over this time, I saw a national community thrive and grow, collaborate broadly and deeply to resolve challenges in bioinformatics, and ultimately create novel research outputs.
Firstly, I feel fortunate that I was able to support and contribute to the GAP effort, as it is an ambitious program of work that has brought together a national community of researchers, bioinformaticians, project managers, facility staff, and infrastructure specialists from research institutes, herbaria, data production facilities, computational facilities, and universities across Australia, and included an on-going international collaboration with the Plant and Fungal Tree of Life (PAFToL) Initiative.
Secondly, while the community is itself an achievement, and will underpin future work in Australian plant genomics, I think it's also important to highlight and celebrate the genuine drive and energy that the GAP teams bring to pushing the boundaries in sample preparation and bioinformatics, to improving the metadata and data offerings that underpin plant genomics, and to making their foundational work accessible and understandable for a broader research audience.
A few key highlights specific to bioinformatics come to mind immediately:
Containerised Nextflow workflows (read the paper) that streamlined the reuse of the software set required for the GAP phylogenomics aspect
The detailed integration and validation of metadata that accompanies the thousands of GAP data entries that are progressively being added to the European Nucleotide Archive.
The successful convergence of GAP bioinformaticians on supercomputing resources at the National Computational Infrastructure, supported by the ABLeS program, and the step change in capability and throughput that resulted from this convergence.
It was both wonderful and humbling to see the first draft version of a phylogenomic tree for Australian flowering plants, the Australian Angiosperm Tree of Life (AAToL).
I can’t wait to see the future successes that GAP will make possible, and in particular the next stage of AAToL.
Managing a Bioinformatics Core Facility Workshop
Late last year, we were lucky enough to be selected to attend the 2023 EMBL-EBI Managing a Bioinformatics Core Facility Workshop held at the Wellcome Sanger Genome Campus in Cambridgeshire, UK.
By DR DEANNA DEVESON LUCAS, MANAGER (BIOINFORMATICS), MONASH GENOMICS AND BIOINFORMATICS PLATFORM
And DR GEORGINA SAMAHA, BIOINFORMATICS GROUP LEAD AT THE SYDNEY INFORMATICS HUB, UNIVERSITY OF SYDNEY
Late last year, we were lucky enough to be selected to attend the 2023 EMBL-EBI Managing a Bioinformatics Core Facility Workshop held at the Wellcome Sanger Genome Campus in Cambridgeshire, UK. We joined 13 other participants from around the globe (Aus, UK, Europe, Middle East, North and South America!) for a whirlwind 3-day immersive course on all things bioinformatics facility management.
Dee is the Bioinformatics Manager at the Monash Genomics and Bioinformatics Platform, Monash University, and Georgie is the Bioinformatics Group Lead at the Sydney Informatics Hub, University of Sydney. We each manage teams of bioinformaticians and developers supporting life science researchers in all things -omics and bioinformatic training. As members of the Australian BioCommons National Training Cooperative, we had previously only ever met over Zoom, but the EMBL-EBI workshop allowed us to finally meet in person. We were also joined by fellow Australian, Jason Li, who is the Bioinformatics Core Facility Manager at the Peter MacCallum Cancer Center.
Bioinformatics core facilities play an essential role in advancing scientific discoveries as hubs of expertise across different institutions. These facilities are integral components in hospitals, research organisations, and universities and we support researchers in extracting meaningful insights from biological data. As the research landscape changes and more and more of us are applying bioinformatics to our experiments, bioinformatics core facilities have to stay ahead of the curve and adapt to emerging technologies, methods, and research priorities.
Throughout the workshop, we explored a variety of topics that are integral to the success and sustainability of our organisations and the services we provide. These included:
Understanding the dynamic landscape and how we adapt to the changing needs of the life science community
The intricacies of service design and how we can better understand our user needs
Exploring strategies to secure funding and managing finances to ensure our services are sustainable
Nurturing a positive working environment and supporting happy bioinformaticians
Assessing and maximising the impact of our facilities on research outcomes
Sharing various project management techniques
We started with a history of bioinformatics, the changing nature of data and analyses, and how these changes require an ever evolving and adaptable facility.
We learnt how to approach issues from different angles, evaluate the user experience and discussed how we could support our teams to ensure they are happy and fulfilled bioinformaticians.
We had extensive collaborative and networking opportunities throughout the course. Interacting with fellow participants hailing from different organisations across the globe provided a unique perspective. Despite our differences and the geographical distances that separate us, we discovered the threads that bind us together were remarkably consistent and we learned a lot from one another. This realisation underscored the universal nature and current realities of bioinformatics. When we weren’t talking all things bioinformatics we had a fantastic team dinner at the nearby village of Whittlesford at the Tickell Arms.
This was a fantastic opportunity to not only upskill but to expand our Bioinformatician Managers network!
If you are interested in finding out more, check out the workshop materials. EMBL-EBI are running the course again in November 2024, we urge other core research facility managers to apply to attend. It’s a fantastic opportunity to not only invest in your professional growth but also to expand your bioinformatics network!
High-altitude hacking
The Australian Outpost of the 2023 BioHackathon struck me as a great opportunity to brush up on my coding skills!
By Siyuan Wang, Symbio Labs
I was reading the BioCommons monthly newsletter when I saw a call out to go to the Australian Outpost of the 2023 BioHackathon. It struck me as a great opportunity to brush up on my coding skills - my current role doesn’t require in depth bioinformatics coding, but I love to code! I write code to solve small but tedious problems that I come across all the time.
When I arrived in Brisbane, I was blown away by the view from our hacking room and made sure to take some photos of the city landscape. It was an inspiring space to work with the group from around Australia, and to link up live online with the European participants.
Once we started hacking the first thing I needed to do was identify the challenges in our project. There was lots of reading about new bioinformatics tools that I hadn’t come across before. Then it was straight into some good old-fashioned problem solving using Python and git. I enjoyed working as a big collaborative team - it was a nice change of pace from my usual work which is usually in smaller groups. I even got a chance to dabble in web development and get creative!
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. I would definitely recommend others get involved next year!
Above: A selection of scenic photos I took in Brisbane.
Green Training: What’s the real impact of your events?
As a training coordinator I’m often asked about the impact of our training on people and their ability to achieve their scientific goals. But what about the environmental impact of our events?
By Dr Melissa Burke, Australian BioCommons
As a training coordinator I’m often asked about the impact of our training on people and their ability to achieve their scientific goals. But what about the environmental impact of our events?
The concept of green training was the focus of a dedicated session at this year’s Bioinformatics Education Summit, which brings together a global community of trainers and educators to develop and share guidance and best practice. The session had us discussing factors that contribute to the environmental impact of training, brainstorming green training solutions, and developing ideas for ensuring that green training policies are equitable and fair.
Encouragingly there are already a number of resources and case studies (e.g. ISCB and EMBL environmental policies) that can be used as inspiration when considering your own green training approach. Common strategies for reducing the environmental impact of bioinformatics training events include encouraging the use of sustainable transport, reducing waste and improving compute efficiency are common targets.
A notable theme from the Bioinformatics Education Summit was one of balance and equity. Choosing greener training/compute options requires money and time and can have other societal impacts. The ability to choose green options (whether as an individual or organisation) is dependent on the same factors that influence diversity, equity and inclusion.¹
For example, switching a workshop to virtual mode can seem like a quick win for the environment. It reduces travel, resources needed, and food waste from catering.² But virtual events forgo the benefits of in-person interactions and those joining from far away still face time zone inequities that can have negative impacts on health and wellbeing.²’³
So how do we save the environment while still providing great training experiences for all?
There is no one-size-fits-all solution. Instead we keep asking questions, get creative and take it one step at a time.
If you’re looking to reduce the environmental impact of your bioinformatics training events, you and your team can start by asking yourselves the questions posed at the Bioinformatics Education Summit:
What are the sources of impact?
How could this impact be reduced?
What are the challenges/barriers to achieving this goal?
What are the trade-offs?
And a bonus question that I’ll keep asking myself in my professional and personal life after listening to the discussions around equity at the Bioinformatics Education Summit: how can we equitably share this responsibility across the community?
The Bioinformatics Education Summit is an annual meeting that provides a platform for the global training and education network to discuss, develop and share guidance and best practice for training and education in bioinformatics.
Resources and guidance
EMBL
ISCB
Green compute resources
References
1. Jackson, S. Yale Experts Explain Intersectionality and Climate Change. https://sustainability.yale.edu/explainers/yale-experts-explain-intersectionality-and-climate-change (2022).
2. Wu, J. et al. Virtual meetings promise to eliminate geographical and administrative barriers and increase accessibility, diversity and inclusivity. Nat. Biotechnol. 40, 133–137 (2022).
3. Jasper, S. The effect of time zone disparity on the performance of dispersed innovation teams. (RMIT, 2019).