Multi-model 3D visualisation enhances Nextflow pipeline for protein structure prediction

Predicted protein structures for LmrP visualised using the proteinfold pipeline

Advances in AI are taking protein structure predictions to a whole new level, accelerating research and enabling deeper analysis of protein structure and function. The nf-core community is embracing these developments by building the Nextflow proteinfold pipeline that integrates models such as Alphafold2, Colabfold and Esmfold and simplifies their use on a variety of computing infrastructures. 

BioCommons’ Dr Ziad Al Bkhetan, Product Manager - Bioinformatics Platforms and Australian Nextflow Ambassador, identified an opportunity to optimise the existing nf-core proteinfold pipeline for Australian researchers using the Australian Nextflow Seqera Service. Ziad initiated this effort by reaching out to the original developers from the Center for Genomic Regulation (CRG) in Spain with an offer to reconfigure the pipeline and add new features. This sparked an international collaborative effort that connected researchers and experts from Australian BioCommons, the CRG, the Sydney Informatics Hub (SIH) at the University of Sydney and the Structural Biology Facility (SBF) at UNSW, at several hackathons and summits to enhance the pipeline. The enhanced, community-driven pipeline is now available to all through nf-core’s curated set of open‑source analysis pipelines. 

The pipeline borrows a useful reporting and visualisation feature already implemented in Galaxy Australia. Front-end developer for BioCommons, Minh Vu, augmented the pipeline to implement this feature which allows the parallel execution of multiple models and generation of reports that visualise the resulting structures simplifying comparison and benchmarking of the outputs. Several state-of-the-art tools such as AlphaFold2, ColabFold, ESMFold are included in the pipeline with additional models including RoseTTAFold-All-Atom, HelixFold3, Boltz, RosettaFold2NA and AlphaFold3 to be added soon.

The ability to run different models through the pipeline without writing new code removes the impediment of command line or complicated compute infrastructure. Reflecting on the project in the Nextflow Podcast, Phil Ewels, Product Manager for Open Source at Seqera, said:

 “With almost no setup and no real prior experience, you can run these state of the art models and compare them all in a dynamic visual report. That’s pretty amazing.”

While it is designed to integrate with Seqera Platform, there’s no requirement to use it that way. Running the Nextflow pipeline on the command line gives the exact same reports. The code is freely available for others to use or improve via the nf-core repository of pipelines.

Ziad’s presentation about the collaboration and these new features was spotlighted as a highlight of the recent Nextflow Summit in Seqera’s Nextflow Podcast. Bioinformatics Engineer at Seqera, Dr Florian Wünnemann acknowledges there is great value in improving shared resources:

 “I think it really represents the best of the Nextflow community: they are developing tools and not just keeping it for themselves, but directly giving them back to the larger community.”

Rob Syme, Scientific Support Lead at Seqera Labs, believes the work speaks to the Nextflow and Seqera ethos of giving scientists and researchers the tools they need to build other tools.

“I love this project: it was an amazing outcome that required no input from Seqera or Nextflow. Yes, Seqera Platform could absolutely build an alignment viewer into the platform, but it wouldn’t be as good as if researchers themselves develop it. It wouldn’t be as good as the one that Ziad and the team have developed because research moves so incredibly quickly.” 

The collaboration within the international nf-core community has been a rewarding experience for all involved parties, and CRG has forged a new working relationship with BioCommons to continue development and maintenance of the pipeline. CRG’s Dr Cedric Notredame said of the experience:

“The collaboration with BioCommons has been so valuable. It has showcased the effectiveness of nf-core as a collaborative tool. Thanks to this framework, all of our teams were able to simultaneously contribute to the pipeline with minimal technical coordination. The pipeline is now one of the most complete go-to resources, covering the needs of a wide community of biologists interested in structural aspects of genomics.”

The improvements made to the visualisation code during the project will also be fed back into the Galaxy codebase. BioCommons’ close connections with research communities means that the national Structural Biology Computing community is now testing and finessing the pipeline, and supporting the creation of user documentation.

Sharing what’s been learnt through a publication about the nf-core/proteinfold pipeline is on the horizon, and a pilot Australian ProteinFold Service is under development.

Nextflow workshop combines benefits of hands-on training and community building

BioCommons’ Nextflow for the life sciences workshop heralds a return of our dispersed model of training that combines the benefits of in person and online events to enable access to experts and foster local connections that are essential for continued learning. First pioneered in 2019, this model has been successful in ensuring scalable and more equitable delivery of short-course bioinformatics training across Australia and has been adapted internationally.

Nextflow for life sciences workshop participants will join in person satellite sites at host universities and research institutes across Australia where they will connect with peers and be supported by experienced local facilitators as they put their new Nextflow skills into action. Each of these sites will connect online with Nextflow experts and lead trainers Fred Jaya and Dr Michael Geaghan at the University of Sydney’s, Sydney Informatics Hub who will introduce key concepts and demonstrate how to use fundamental Nextflow elements to develop, execute, and debug a scalable multi-step life science workflow.

Find out more and apply for the workshop. Applications close 27 June 2025.

This workshop is made possible by an exceptional network of facilitators and trainers from the national Bioinformatics Training Cooperative.

WorkflowHub: a registry for computational workflows

A new paper in Nature Scientific Data describes a public and inclusive registry dedicated specifically to the sharing of computational workflows: WorkflowHub.

Australian BioCommons’ Research Community Engagement Lead (Proteins / Metabolites / Workflows), Dr Johan Gustafsson, is the lead author of a stellar group of international experts. They have worked hard on their shared passion for a unified registry for all computational workflows that links to community repositories, and supports both the workflow lifecycle and making workflows findable, accessible, interoperable, and reusable (FAIR).

The WorkflowHub registry is designed to allow any scientist, regardless of expertise level, to contribute and share computational workflows. It indexes workflows from any scientific domain, in any format, in any workflow language, regardless of whether it uses a workflow management system and supports users to increase the FAIRness of their workflows.

By interoperating with diverse platforms, services, and external registries, WorkflowHub adds value by supporting workflow sharing, explicitly assigning credit, enhancing FAIRness, and promoting workflows as scholarly artefacts. The registry has a global reach, with hundreds of research organisations involved, and more than 800 workflows registered.

The paper describes how WorkflowHub’s structure, design, standards, community engagement, and continued evolution support:

1) collaboration, sharing and credit for workflow developers, projects, and consortia;

2) integration with added-value services, platforms, and capabilities that support the workflow life cycle (i.e. creation, version control, execution, maintenance, reuse and citation); and

3) wizards and inbuilt features that ease the process of sharing workflows alongside the constellation of associated digital artefacts that give a workflow its scientific context.

Read the paper in full Gustafsson, O.J.R., Wilkinson, S.R., Bacall, F. et al. WorkflowHub: a registry for computational workflows. Sci Data 12, 837 (2025). https://doi.org/10.1038/s41597-025-04786-3

Join our co-working session on 24 June to try out WorkflowHub for yourself.

New seminar series ignites curiosity and builds practical AI skills in the life sciences

AI is reshaping life sciences by enabling researchers to analyse complex datasets, automate workflows, and gain deeper insights into biological processes. Australian BioCommons is supporting the community to adopt these technologies through a series of training events that explore what’s possible and build skills in using AI effectively.

We’ve invited a diverse range of your peers from across academia and industry to share their experiences of using AI in the life sciences. Between June and September you’ll hear how AI is being used to push boundaries, solve problems, and reimagine the way we do science. From multi-omics analysis to drug discovery, structural biology and the ethics of AI in science, they will explore diverse applications across the life sciences, focusing on the stories, insights, and experiences behind the research.

Register for the webinars

In August, our online workshop Machine learning in the life sciences will provide a hands-on opportunity to compare and contrast commonly used algorithms for constructing predictive models, explore some of their trade-offs and identify types of scenarios in which they can be applied.

In case you missed it, Australian BioCommons’ AI Technical Lead, Dr Benjamin Goudey, recently broke down AI concepts, clarified key terminology, and showcased real-world examples in this recorded webinar: Deciphering AI for the Life Sciences. 

AI is a fast evolving field so rest assured that further events are in the pipeline. 

Browse all upcoming training and events 

Australia's inaugural nf-core Hackathon Outpost boosts local Nextflow capability

The first-ever Australian satellite site of the international nf-core Hackathon has just taken place in Sydney. Seventeen participants from across the country came together to collaborate on cutting-edge Nextflow projects. This marked a significant step in strengthening Australia’s Nextflow and nf-core community, fostering new collaborations between researchers, bioinformaticians, and Nextflow enthusiasts.

International registrations for the 2025 nf-core Hackathon almost reached 1000, with about half opting to join remotely and the remainder spread across 44 sites globally. The organisers were thrilled to finally have an Australian site. Thanks to our time zone, we were among the first to kick off each day of asynchronous work, along with colleagues across the ditch in Aotearoa New Zealand. 

Australian BioCommons arranged for key participants including multiple Nextflow Ambassadors from multiple cities to join our local hosts, Sydney Informatics Hub at the University of Sydney. Participants represented Pawsey Supercomputing Research Centre, National Computational Infrastructure, Peter MacCallum Cancer Centre, QCIF, Queensland University of Technology, Sydney Informatics Hub, University of NSW, and Australian BioCommons. 

The group spent three days at Moore College, a fantastic venue with an open workspace and an expansive terrace with city views - providing an ideal setting for focused work, brainstorming, and cross-team collaboration. While the hackathon was all about accelerating nf-core developments, it was also a valuable chance for collaboration outside of participants’ regular networks. Seqera sponsored our working lunches, but the Newtown cafe and restaurant scene ensured participants stayed well-fueled throughout the whole hackathon!

Over the course of three productive days the group divided up to tackle key projects in Nextflow development, including:

• Working towards a new release of the nf-core ProteinFold pipeline; 

• Developing a Nextflow for HPC training for Australia’s national supercomputers, NCI’s Gadi HPC and Pawsey’s Setonix HPC;

• A nf-test working group to write and apply unit tests to existing institutional pipelines.

As well as progressing some locally important projects, the gathering was a great opportunity to discuss Nextflow training collaborations and how we can work together to ensure more Australians can access the Nextflow skills and resources they need. Keep an eye on our training events listings to see the outcome of these new national relationships.

We are so grateful to the Seqera team and the nf-core community for their enthusiasm and efforts to welcome the Australian satellite site of the hackathon. And massive thanks to the participants who contributed their time and energy to make this event both productive and fun! With the success of this first Australian outpost, we’re already looking forward to next year’s nf-core Hackathon. 

Australian palaeoenvironments and biodiversity to be reconstructed through metagenomic analysis of sedimentary ancient DNA by national collaboration with Indigenous partners

Dr Vilma Pérez uses environmental DNA techniques to understand when and how environments have changed and responded to disturbances

A fascinating new project now has access to the specific computational resources required to build high resolution records of Australia’s changing ecosystems over the past millennium. The research will reconstruct Australian palaeoenvironments and biodiversity using metagenomic analysis of sedimentary ancient DNA collected from mainland Australia and the Torres Strait Islands as part of codesigned projects involving leading Australian researchers and Indigenous partner organisations. Streamlined bioinformatics analysis pipelines will be essential to process the large volume of samples expected to come in from this collaboration.

Sedimentary ancient DNA (sedaDNA) analysis is a transformative tool for studying past biodiversity and its responses to environmental, climatic, and human-induced change. The project aims to build capacity for the growth of sedaDNA research in Australia by automating bioinformatic analyses into a single Nextflow pipeline that can easily produce a robust and reproducible taxonomic profile of both modern and ancient target species found in sediment samples. BioCommons was keen to support the research with access to both ABLeS and our Australian Nextflow Seqera Service. 

This project is part of the ARC Centre of Excellence for Indigenous and Environmental Histories and Futures (CIEHF) which seeks to create a lasting impact by integrating Indigenous and Western knowledge frameworks to model environmental, cultural, and historical change in Australia over the past millennium and into the near future. 

Dr Vilma Pérez is an environmental microbial ecologist at the Australian Centre for Ancient DNA, The University of Adelaide, who can now access the national computational infrastructure she needs for her research after being onboarded to BioCommons’ ABLeS and Seqera services. Vilma's expertise in using environmental DNA techniques to understand when and how environments have changed and responded to disturbances will be put to good use in CIEHF’s novel genetics research program.

Led by CIEHF Chief Investigator Assoc Prof Ray Tobler from the Evolution of Cultural Diversity Initiative at the Australian National University, the research program will use high-resolution landscape genomic analyses of selected Australian native flora and fauna, as well as ancient DNA recovered from archaeological sediments (sedaDNA).

This work will help reconstruct past Australian ecosystems to understand how biodiversity, from microbes to plants and animals, has changed over time, and how it has responded to environmental shifts, including Indigenous Australian landscape management practices that have helped care for Country for thousands of years.

Gaining access to the right computing infrastructure is one thing, but appropriate computing and data management mechanisms are needed to ensure that Indigenous genomic data resources are ethically managed to the benefit of Indigenous Australians. Mutual partners, Bioplatforms Australia, were able to connect CIEHF with colleagues at the National Computational Infrastructure (NCI) who are working with the National Centre for Indigenous Genomics (NCIG) to host their sensitive sequencing data. Given Indigenous genetics research requires unique ethical approaches, NCIG is leading the way in building a genome resource for the research community under Indigenous Governance and will no doubt have many insights to share. 

As part of our ongoing support for CIEHF, Dr Ziad Al Bkhetan, Product Manager - Bioinformatics Platforms at BioCommons, and Dr Kelly Scarlett, Manager - Partnerships and Engagement at Bioplatforms Australia will participate in an upcoming sedaDNA workshop hosted by CIEHF researchers at the University of Adelaide.

This workshop sits within the Genomics research stream which is part of a suite of nine chosen to ensure a holistic, interdisciplinary approach. Find out more about how CIEHF’s research streams are addressing unique environmental, cultural, and historical complexities of Australia through an integrated approach, leveraging both Indigenous knowledge systems and researcher’s fields of expertise. 

Productive connections in the global Nextflow community forged by co-working

A group of Nextflow enthusiasts will come together in Sydney to take part in the global nf-core hackathon in March. By hosting the first Australian satellite site, we hope to unlock new opportunities for both national and international collaboration.

The global nf-core community curates a set of open‑source analysis pipelines built using Nextflow and they connect regularly through in person and online events. For the first time, the international hackathon’s network of live sites is extending to Australia, with the Australian outpost of the 2025 nf-core hackathon facilitating participation during our waking hours across 24-26 Mar 2025. The group will work on a variety of projects including development of training materials and nf-core workflows alongside our five local Nextflow Ambassadors and their international colleagues.

BioCommons’ Product Manager, Bioinformatics Platforms, Dr Ziad Al Bkhetan is a Nextflow Ambassador who has experienced the value of forging strong relationships in the global Nexflow community. In his work leading the Australian Nextflow Seqera Service, Ziad identified that Proteinfold, an existing nf-core pipeline for Protein 3D Structure prediction, had great potential for Australian researchers. 

Ziad identified several ways to improve Proteinfold and connected with the original developers at the Centre for Genomic Regulation (CRG) in Spain, to reconfigure the workflow, add new features, and contribute the updates back to nf-core. Ziad’s demonstration of the new tool at the last Nextflow Summit created excitement in the Nextflow community. Seqera, the team behind Nexflow, was delighted that their community-driven approach is resulting in new tools being developed by people at the research interface. CRG was pleased to see that their contribution to the community facilitated a new working relationship between their Spanish biomedical research institute and Australian BioCommons. Ziad and the team from CRG will continue to work on their workflow at the nf-core hackathon, and welcome contributions from any other community members. 

We’re looking forward to connecting with the Seqera team and international peers at the nf-core hackathon to develop workflows and training materials  asynchronously. There is a growing list of projects being proposed and we can expect that the range will expand as teams around the world get to work.

Finding the right collaborator can fast track a project like nothing else, and specialist fields of research almost guarantee your perfect match will be on the other side of the world. We’ve already seen how strategic events can bring global developer communities together to forge valuable new relationships in the Nextflow community, and hope to catalyse more of these opportunities. 

Let us know if you are interested in joining the nf-core hackathon: Australian Outpost.

New bioinformatics pipeline for the identification and detection of viral genomes from Oxford Nanopore sequencing

An example output plot generated by the pipeline

Pathogenic viruses and viroids infecting plants can result in significant economic and ecological losses. In recent years, advances in Oxford Nanopore Technologies (ONT) have enabled real-time sequencing of long sequences through portable sequencers and thus offered a new avenue for plant virus diagnostics and research. A team from Queensland University of Technology (QUT) led by Assoc Prof Roberto Barrero and the Queensland Cyber Infrastructure Foundation (QCIF), have developed a new bioinformatics pipeline that facilitates the detection of viruses and viroids from both amplicon and metagenomic ONT data using different analytical strategies.

The pipeline called ONTViSc (ONT-based viral screening) can: 1) perform a direct search on the sequenced reads, 2) generate clusters, 3) assemble the reads to generate longer contigs or 4) directly map reads to a known reference. The pipeline is written in Nextflow, ensuring that it is reproducible, scalable, and can be run on a diverse set of compute infrastructures. It was written by Dr Maely Gauthier and tested by Dr Magda Antczak. 

The workflow was developed in consultation with both researchers and diagnosticians at the Australian Government’s Department of Agriculture, Fisheries and Forestry (DAFF) to understand how it would best cater to their needs based on their current and projected internal usage of ONT, as they transition some of their processes to the new technology. The pipeline has been validated with edge samples and helped resolve the complete genome of novel plant viruses.

The ONTViSc pipeline is now available for anyone to deploy or adapt through QUT’s GitHub repository, and the how-to guide is available within the Australian BioCommons How-to Hub. 

Magda utilised the Australian Nextflow Seqera Service to develop, optimise and run the ONTViSc pipeline, and spoke about the benefits of this fully subsidised service in December at the Australian Bioinformatics and Computational Biology Society (ABACBS) National Seminar Series.

The completion of this pipeline development has led to an independent nation-wide project aimed at transforming biosecurity diagnostics by making standardised bioinformatics workflows and interactive reports accessible to all DAFF biosecurity sites. The project, DNA to Decisions: Concise communication of genomics data for easier decision making is supported by a partnership between Australian BioCommons (as part of Workflow Commons), QCIF, QUT and DAFF.

The Australian Nextflow Seqera Service: Your one-stop shop for Nextflow workflows

A new service provides access to a centralised command post for Australian researchers to manage, launch and monitor their Nextflow workflows. This subsidised access to Seqera Platform is now available through a licensing agreement between Seqera and Australian BioCommons.

Researchers can run workflows on the Australian Nextflow Seqera Service using their existing allocations at their preferred compute infrastructure, including local high-performance computers (HPCs) or commercial cloud services. Alternatively, national compute resources at Tier 1 facilities are available through the complementary Australian BioCommons Leadership Share (ABLeS). Dr Magdalena Antczak, Bioinformatician at QCIF, found this connection particularly helpful:

Thanks to the resources allocated to us by the ABLeS program, we were able to launch the ONTViSc pipeline detecting viruses from plants from within the Australian Nextflow Seqera Service. We could test the pipeline thoroughly using multiple high-performance computing infrastructures and cater for users without easy access to bioinformatics services.

Out-of-the-box configurations for running Nextflow pipelines on Pawsey Supercomputing Research Centre’s Setonix and National Computational Infrastructure’s (NCI’s) Gadi are available. Or if research groups need a more bespoke approach, extensive technical documentation and the friendly user guide will help tailor the Australian Nextflow Seqera Service to their needs.

Dr Julie Iskander, Lead Research Computing Engineer at WEHI, has seen the benefits for researchers first hand:

WEHI’s Research Computing Platform Engineering team supports WEHI researchers through software engineering services to build tools and pipelines. Seqera Platform has helped us a lot. We've been able to invite our researchers to jump in and see if the platform meets their needs. With the support of the BioCommons, we've had 15 researchers across 7 of our different research groups try it out. It's made launching pipelines easy for researchers who are not familiar with linux systems and command line. This helps them to independently run complex workflows on the HPC, with minimum knowledge of its underlying complexities.

WEHI was one of the 33 groups across 16 Australian research institutes taking part in BioCommons’ successful two-year pilot program, supported by Pawsey, NCI, Sydney Informatics Hub, Queensland Cyber Infrastructure Foundation (QCIF) and the University of Melbourne. Over that time, Seqera worked with BioCommons to understand how to best support the local Nextflow community and match Australian researchers’ sophisticated usage of the workflow management and data analysis environment, Seqera Platform.

The Australian Nextflow Seqera Service is fully subsidised for groups of up to three users to work collaboratively in a dedicated workspace. Larger organisations can explore the service at no cost by bringing an unlimited number of users to their dedicated workspaces for their first year of use (annual fee applies thereafter).

The Australian Nextflow Seqera Service is a key component of BioCommons’ vision to build an ecosystem of data analysis infrastructures that empower breakthrough discoveries.

Find out more about the Australian Nextflow Seqera Service and register to get started today!

The Australian Nextflow Seqera Service is operated by Australian BioCommons in collaboration with Pawsey, NCI, and Seqera. It is hosted on Amazon Web Services and supported by Bioplatforms Australia via NCRIS funding.

Advancing the Nextflow conversation: Connect with Seqera’s Lead Developer Advocate in Melbourne

Dr Geraldine Van der Auwera, Lead Developer Advocate at Seqera, is visiting Melbourne in September to strengthen ties and support the growth of bioinformatics activities in Australia. She will meet with key stakeholders and deliver a public webinar to share the latest technical innovations and opportunities to engage with Nextflow and Seqera Platform (formerly Nextflow Tower).

The ongoing relationship between Australian BioCommons and Seqera is uplifting Australian researchers to access and deploy Seqera’s products, including Nextflow and Seqera Platform. Geraldine is visiting Melbourne to discuss future Nextflow-related activities with BioCommons and the Australian Nextflow Ambassadors, Dr Georgie Samaha and Dr Ziad Al Bkhetan. They want to know if an informal Australian Nextflow network would benefit life scientists and bioinformaticians. Share your thoughts by filling out a brief survey: Assessing interest in an Australian Nextflow network.

You can hear more from Geraldine when she delivers a BioCommons webinar Building the future of bioinformatics with Nextflow: Technical innovation, community engagement, and career development opportunities on 19 Sep 2024.  You can also meet with Geraldine in spare moments around her GA4GH Plenary attendance. Please email comms@biocommons.org.au if you would like to be connected.

P.S. If you’re looking to get hands-on with Nextflow, apply to join the Hello Nextflow! workshop on by 10 September. This workshop is being offered by BioCommons, Seqera and the Sydney Informatics Hub.