Mentor program breaking down barriers with Nextflow/nf-core

Dr Georgina Samaha, Bioinformatics Group Lead at the Sydney Informatics Hub and BioCommons team member.

A mentorship in the Nextflow and nf-core program has been awarded to Australian BioCommons bioinformatician Dr Georgina Samaha, Bioinformatics Group Lead at the Sydney Informatics Hub. The highly competitive Nextflow/nf-core mentorship program will pair Georgie with an experienced developer to work closely on a project that she is particularly passionate about: breaking down barriers that prevent life sciences researchers from using high performance computing (HPC). 

The ever-increasing scale of life sciences data means that researchers need to process or analyse their data with large-scale compute resources. This can be a daunting process, particularly for those with less experience writing code or interacting with computers on the command-line interface. Georgie plans to address these challenges:

“I will create new resources and share my learnings about Nextflow/nf-core with the broader life science research and bioinformatics communities to make their lives easier, give them a starting point and increased confidence in approaching the difficult and intimidating aspects of their work on HPCs.”

Georgie is heavily involved in improving access to command-line infrastructure for life sciences researchers as part of the BioCommons Bring Your Own Data Expansion Project. She applied to the Nextflow/nf-core mentorship program as she frequently encounters researchers who need her help to run bioinformatics pipelines on HPCs. nf-core offers community-supported reproducible pipelines that simplify data processing. These pipelines are popular in the bioinformatics community, but researchers still face challenges in using them such as understanding the resource requirements and running the pipelines efficiently. Georgie’s project aims to address these challenges to make life sciences researchers’ lives easier. She also aims to demonstrate to national HPC providers that there is significant value in improving access to large-scale compute resources for life sciences researchers.

Georgie expects that her involvement in the mentorship program will greatly increase the level of support she can offer to researchers, plus provide her valuable experience coding in Nextflow. Georgie will bring this newfound expertise to her role at Sydney Informatics Hub and the BioCommons to empower the researchers she works with, plus share her knowledge with partners including QCIF, NCI and Pawsey.

Georgie’s mentorship started in June and will run until the end of September 2023. You can find out more about the Nextflow/nf-core mentorship program at the nf-core website, and stay tuned to hear from Georgie later in the year!

Announcing the inaugural Simon Gladman Travel Grant

The contributions of the late Simon Gladman to Galaxy will be honoured by an annual award in his name. Galaxy Australia’s talented Technical Lead and everybody’s mate, Simon was sorely missed at GCC2023, where he was remembered with several tributes.

Simon was passionate about Galaxy and connecting with people, and was very excited to be organising the first international Galaxy Community Conference (GCC) to be hosted in Australia. He was celebrated at GCC2023 with the announcement of the inaugural Simon Gladman Travel Grant. The grant of AUD $5,000 will be awarded annually to an Australian citizen who is participating in a Galaxy community event. 

If you share Simon’s passion and want to contribute to Galaxy you’re encouraged to apply for the Simon Gladman travel grant.

Funding awarded to develop an Australian Cardiovascular disease Data Commons

Development of the Australian Cardiovascular disease Data Commons (ACDC) is underway thanks to a successful Medical Research Future Fund (MRFF) Critical Research Infrastructure bid. As part of the recent funding announcement for new medical technology and research facilities, the project received $3M to develop an Australian Cardiovascular disease Data Commons that is controlled, secure, scalable, internationally integrated and connected with the world's best-practice analysis platforms. The ACDC will pave the way for researchers to make new mechanistic insights and identify potential markers for coronary artery disease, plus facilitate a translational pipeline to ensure new discoveries are deployed to clinical practice. 

Coronary artery disease is the leading cause of premature cardiovascular death in Australia, and results in serious disability for survivors. It is extremely difficult to detect and many patients have no warning symptoms, despite the underlying atherosclerotic plaque developing over several years. The advance of data-intensive biomarker research techniques such as genomics, metabolomics, proteomics and immuno-phenotyping along with image processing, machine learning, and systems biology pipelines is a golden chance to make the next leap in the protection of patients at risk of coronary artery disease. However, there is currently no efficient way to identify cross-study cohorts for combined analysis. The ACDC will enable combined analysis by providing researchers with access to pooled data from over 400,000 individuals across more than 18 clinical cohorts within Australia.

The successful funding bid was led by a multi-organisational team comprising the Australian BioCommons, the Baker Heart and Diabetes Institute, Bioplatforms Australia, the University of Melbourne, the University of Sydney, 23Strands, CSL Limited and 18 cohort custodians. The BioCommons team are leading the implementation of the digital infrastructure underpinning ACDC, using software systems such as the Gen3 data commons from the Centre for Translational Data Science at The University of Chicago. The digital infrastructure that ACDC yields will no doubt benefit other data intensive precision medicine programs.

The ACDC project is funded for the next four years, with the first three large datasets soon to be integrated into the platform. The team at Australian BioCommons are extremely excited to be part of the ACDC project and can’t wait to get started! Learn more about the developing Australian Cardiovascular disease Data Commons now.

New partnership ensures sustainability of DReSA training registry

The Digital Research Skills Australasia (DReSA) national training registry has found a home in a new national partnership between Australian Research Data Commons (ARDC), Pawsey Supercomputing Research Centre (Pawsey) and National Computational Infrastructure (NCI). This group will take on the management, continued development and maintenance of the service in collaboration with the Australian training community.

BioCommons is an active member of the DReSA Working Group and our events and training materials can be found in DReSA alongside almost 1000 other events and 100’s of training materials. We’ve followed the development of DReSA from idea through to sustainability where BioCommons connections with ELIXIR and their TeSS Training portal proved pivotal in the development of DReSA. The open source codebase of TeSS provided a framework for the development of DReSA, saving considerable time and effort. This has sparked ongoing collaborations between Australia and ELIXIR with developments in DReSA now feeding back into TeSS. 

Our membership of the DReSA working group and the TeSS Scientific Advisory Board puts us in a unique and exciting vantage point to watch the coevolution of these valuable training resources. We are proud to be part of this wonderful example of collaboration around a common challenge involving a large group of Australian organisations and ELIXIR. We look forward to seeing and supporting what comes next for DReSA and TeSS! 

Read more about the future of DReSA in the ARDC, Pawsey and NCI press releases.

The international genetics and genomics community comes to Melbourne

Members of the Australian BioCommons team are attending the 23rd International Congress of Genetics (ICG) from 16-21 July in Melbourne. Meet us at booth 27 to find out about our activities in building bioinformatics infrastructure to support human health, agricultural and environmental science research, and discuss the challenges researchers face. We’ll showcase the services that the BioCommons and our partners offer and we would love to hear your feedback!

As well as visiting our booth, keep an eye out for the BioCommons team in the symposia, and the poster and speciality sessions:

• Associate Director - Human Genome Informatics, Bernie Pope: Ultra-sensitive detection of circulating tumour DNA enriches for patients with higher risk disease in clinically localised prostate cancer (talk on 20 July, 11 am)

• Human Genomics Data Specialist, Marion Shadbolt (poster): Advancing human genomics data sharing in Australia: Highlights from the Australian BioCommons

• Community Engagement Officer, Tiff Nelson (poster): Robust public computational services supporting Genome Assembly and Annotation for Australian researchers

• Bernie Pope (poster): Somatic mutation landscape in a cohort of meningiomas that have undergone grade progression

• Deputy Director, Jeff Christiansen will give an overview of BioCommons services supporting genomics research at approximately 1 pm during the Genetics Society of AustralAsia (GSA) annual general meeting on 19 July

While at the congress, you can also visit our partners the Atlas of Living Australia (ALA), who are providing an early look at the new Australian Reference Genome Atlas interface, plus other Bioplatforms Australia supported facilities including the Australian Genome Research Facility, Ramaciotti Centre for Genomics and the Australian National University Biomolecular Research Facility. 

Registration is still open, so come along and chat with the BioCommons team. We can’t wait to see you there!

Gen3 Community Forum to showcase how the BioCommons uses Gen3

Australian BioCommons partners with the team behind Gen3 at the Center for Translational Data Science, University of Chicago, USA to custom build several data commons for use by large Australian national research consortia. 

We help convene the international Gen3 Community Forum, and the next online event ‘Data Modeling in Gen3 Data Commons’ is coming up on Friday July 7, 6.30 am AEST (check in your timezone). Our Human Genomics Data Specialist, Marion Shadbolt, will deliver a presentation on streamlining Gen3 data dictionaries.

Marion’s presentation will outline progress from the BioCommons’ partnership with the Precision Medicine Flagship of the Australian Cardiovascular Alliance (ACvA). The team have been using Gen3 to develop a data dictionary for the Australian Cardiovascular Disease Data Commons, using a google sheet as input and fully automating the workflow to edit, test, validate and publish Gen3 data dictionaries.

Gen3 can be customised for a wide variety of projects and use cases, and there will be three additional presentations from other data commons operators, discussing how they have created their dictionaries and describing the tools or processes they use for updating and configuring them.

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

Additional details and registration

Genome Lab: The new online workbench for easier data analysis

The new Galaxy Australia Genome Lab interface.

The new Galaxy Australia Genome Lab is now available for use by the Australian genomics community. This customised, user-friendly view of Galaxy Australia provides rapid access to a range of sophisticated genome assembly and annotation resources while retaining the full power of Galaxy Australia.

Genome Lab offers a curated collection of bioinformatics tools, workflows and tutorials tailored to data preparation, genome assembly and genome annotation. The new user-friendly, one-stop-shop within the Galaxy platform is the perfect place for newcomers to data analysis. All relevant tools and workflows come with descriptions and examples of required inputs to help researchers get started. For more advanced users, the full functionality of the Galaxy Australia platform is accessible through the surrounding tools panel and navigation bar. User history, jobs and data quota are shared with the main service, making it easy to switch between Genome Lab and the main Galaxy Australia interface.

Galaxy Australia provides Australian researchers with fully subsidised access to a high-performance computing network through a simple web interface. Researchers are able to undertake reproducible and transparent computational research in an accessible format, without needing any prior command line programming experience. There are over 1,500 pre-installed tools and over 350 workflows with extensive documentation, tutorials and training available. Wanting to simplify access and use by genomics researchers, the Galaxy Australia team developed the Genome Lab interface.

The development of Galaxy Australia’s Genome Lab represents an important step forward in Australian BioCommons activities to support Australian genomics researchers. The Genome Annotation and Genome Assembly Infrastructure Roadmaps identified a need to implement easily accessible platforms that contain all the tools for genome annotation and assembly in one location. The Galaxy Australia team has worked hard to deliver this for the genomics community, and will now continue to gather user feedback to enhance the Genome Lab. Stay tuned for updates, plus releases of other Labs supporting different research domains in the future.

If you are an Australian researcher with an interest in genomics, be sure to try out the new Galaxy Australia Genome Lab now!

New community uplifts bioinformatics trainers in Australia

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

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

• What makes a successful research infrastructure community?

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

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

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

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

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

Australian BioCommons and ELIXIR announce extension of collaboration strategy to 2028

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

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

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

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

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

Notable achievements:  2020 to 2023

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

Training

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

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

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

Tools (including Galaxy)

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

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

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

Compute and AAI (Authentication and Authorisation Infrastructure)

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

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

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

Data (including human data)

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

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

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

Forward facing: 2023 to 2028

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

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

Find out more

ELIXIR and Australian BioCommons Collaboration Strategy 2023-28

ELIXIR’s International Strategy

ELIXIR and Australian BioCommons training collaborations

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

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

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

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

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

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

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

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

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

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

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

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