A new best-practice workflow for easy and efficient genome assembly

An off-the-shelf bioinformatics workflow for genome assembly from HiFi read data is now available and has been specifically tailored for Australian researchers. The new custom-built genome assembly workflow:

• Allows researchers to easily and efficiently assemble genomes from their HiFi read data

• Has a full suite of supporting guides and technical documents for users to follow thanks to the experts at the AGRF and the BioCommons team

• Is easily findable via WorkflowHub.

Assembling genomes from HiFi reads is a common roadblock for researchers. Now, researchers can access a customised solution following a successful collaboration between two Bioplatforms Australia facilities, the Australian Genomics Research Facility (AGRF) and the Australian BioCommons. Dr Kenneth Chan, Bioinformatics Manager at the AGRF, said that:

This custom-built genome assembly workflow provides a standardised approach that follows best practice in terms of workflow design, documentation and user support. Now when AGRF generates HiFi long read sequencing data for researchers we can direct them to this workflow solution with confidence that it will suit their needs.

The workflow is written in NextFlow and employs assembly software specific for HiFi sequencing reads. It features pre-assembly quality control for the raw sequence data, a primary assembly stage using the Improved Phased Assembler from PacBio, and a post-assembly quality control stage.

Outline of the tools and processes within the HiFi genome assembly workflow

Community scale research requires reproducible, best-practice, bioinformatics workflows that can be run on a multitude of computational systems. The new custom-built workflow has been optimised across several national research consortiums, and can run on the Gadi supercomputer at NCI Australia, the Setonix supercomputer at Pawsey, Amazon Web Services, and the in-house computational systems at the AGRF. Looking to the future, the workflow has been prepared for use on NextFlow Tower as the BioCommons and our infrastructure partners are in the process of setting up a national NextFlow Tower service. 

Researchers can find the new workflow easily on WorkflowHub. If you are interested in contributing to future efforts in the workflows space, the Australian BioCommons coordinates a community for computational workflows in bioinformatics. Anyone is welcome to join the conversation and contribute!

The Australian Outpost of BioHackathon Europe is back for 2023!

Do you want to join this year’s BioHackathon Europe but can’t make it to Barcelona? Like we did in 2022, we’re putting together a team who will join from Australia, working with the international participants in their timezone - but from a city closer to home.

This is a unique opportunity to participate in a significant global event and network with your international peers while working intensively on practical coding challenges. We will fly you to Brisbane to work together in a hotel for the duration of ELIXIR’s BioHackathon: 30 Oct to 3 Nov 2023. Participation will require working in the evening, so we will keep the late-night hacking vibes going by linking up live with the team in Barcelona (5pm until about midnight) and enjoying Spanish foods as if we were there!

Projects we’ll be working on:

• Galaxy ENA Upload as an Interactive Tool

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

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

BioHackathon participation aims to:

• Advance the development of an open source infrastructure for data integration to accelerate scientific innovation

• Engage technical people in the bioinformatics community to work together on topics of common interest

• Strengthen interactions, establish and reinforce collaborations through hands-on programming activities.

Alert us asap if you are interested in joining the Australian Outpost of the BioHackathon Europe, including which project/s would you like to participate in and why? When we get a feel for who is interested we will select a team of people and organise our meetup. No need to register for a place on the BioHackathon Europe website - they have reserved places for the Australian Outpost.

Please submit your expression of interest to christina@biocommons.org.au by close of business 11 Sep 2023.

Wrapping up the 2023 Galaxy Community Conference

We have just wrapped up the international Galaxy Community Conference for 2023, where over 130 delegates from 20 countries joined us in Brisbane and online to discuss the latest developments in Galaxy.

GCC2023's inspiring keynote speakers shared how they use Galaxy in their important research into biodiversity and structural biology.

• Dr Carolyn Hogg, University of Sydney: To infinity and beyond – combining genomics and cloud technology to save our species 

• Dr Kate Michie, University of New South Wales: Alphafold2 and the Age of Deep Learning - Recent advances in structural biology

• A/Prof Roberto Barrero Gumiel, QUT: Improving plant industry access to new genetics through faster and more accurate diagnostics of plant viruses and viroids

Galaxy Executive Board member, Michael Schatz, who is a Bloomberg Distinguished Professor of Computer Science and Biology at Johns Hopkins University was encouraged to see that:

“The keynotes really highlighted how Galaxy enables cutting edge science.”

Galaxy Australia team members from BioCommons, Queensland Cyber Infrastructure Foundation (QCIF), University of Queensland, Melbourne Bioinformatics and AARNet presented on topics ranging from monitoring tool health to developing the recently released Galaxy Australia Genome Lab. Dr Gareth Price, Project Lead for the Galaxy Australia service, said that:

“There was fantastic exchange between our team and international colleagues, and wonderful opportunities to engage with the global Galaxy community. GCC was an exhilarating experience and it was inspiring to be surrounded by like-minded people. The team left full of energy to keep improving Galaxy Australia and strengthen their collaborations with the wider Galaxy community.”

While we were hosted by Queensland University of Technology (QUT) at their fabulous facilities at The Cube, the ability to participate remotely was a critical factor in providing a truly international conference. Although he was part of the GCC2023 Organising Committee, Dr Prash Suravajhala, Principal Scientist, Systems Genomics at Amrita University, was unable to travel from India, but was:

“Very excited and happy to be a part of GCC2023 virtually. We witnessed scintillating talks and brainstorming sessions and the virtual attendance was a treat. This was a cherishing moment for me as I guzzled the talks from early morning India time! It has created a great camaraderie.”

Following four days of presentations and training workshops, a three day Collaboration Festival (CoFest) saw participants work on solutions and enhancements in a way that is only possible when the global team comes together. Members worked together to expand the Galaxy ecosystem, with contributions to Galaxy's tool set, documentation, training materials, code base, and much more.

The back of the GCC2023 conference T-shirt featured a tribute to Simon.

Simon Gladman, who was an original instigator and organiser of GCC2023, would have been so proud to see his partner and kids participating in the conference. Simon was remembered with several tributes and his legacy as an innovator, role model, supporter and community connector will continue to be honoured by the renaming of the “Intergalactic Data Commission” to “Simon’s Data Club” and by an annual award in his name.

All GCC2023 presentations will soon be freely available. If you’d like to receive the notification about recordings, and keep up with plans for GCC2024 in Brno, subscribe to the BioCommons eNews or Galaxy Announcements.

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!