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.

New resources power long-running workflows at Pawsey Supercomputing Research Centre

Pawsey’s Setonix supercomputer (supplied by Karina Nunez).

Specialised nodes are now available at the Pawsey Supercomputing Research Centre that are designed to power long-running scientific workflows. Responding to researcher demand, new Workflow Nodes have been custom built on Setonix to optimise and support workflows managed by tools like Nextflow and Snakemake that surpass the regular 96 hour wall-time constraint.

Researchers voiced their challenges in running long workflows, including numerous reports from the BioCommons computational workflows community that they were running out of wall-time - the clock time it takes for a computation to run from start to finish. One of these researchers was Lauren Huet, Bioinformatics Research Officer at the Minderoo OceanOmics Centre at UWA:

Our Ocean Genomes project is addressing a key gap where over 95% of marine vertebrates lack sequenced genomes. Building such a comprehensive reference genome library requires intensive compute power, and the workflows can be quite long. This project would not be possible without the capacity to scale up to process tens or hundreds of genomes in parallel.

Dr Sarah Beecroft, Life Sciences Supercomputing Specialist at Pawsey, led the team effort to build dedicated Workflow Nodes on Pawsey’s Setonix - the most powerful research computer in the Southern Hemisphere. 

Setonix’s Workflow Nodes provide a stable and robust environment for workflow orchestration. Users can launch their master jobs interactively and keep their sessions alive for extended time periods, enhancing both productivity and performance. I’m really excited to see the new research that is enabled!

Lauren and the OceanOmics team are already benefiting greatly from the Workflow Nodes:

It’s been a game-changer for our research! The nodes enable us to run Nextflow pipelines directly in the terminal, offering unparalleled flexibility for developing and testing our workflows. The capability to execute long-running pipelines without interruptions has significantly increased our throughput, allowing us to produce results faster and more efficiently.

As a member of the BioCommons BioCLI project, Sarah is passionate about making command-line infrastructure accessible and well documented. Together with other supercomputing experts, the team has produced a new comprehensive technical user guide for users looking to run their workflows on the Setonix Workflow Nodes.

Learn how to run workflows on the Workflow Nodes in Pawsey’s user support documentation, or join the next meeting of the BioCommons computational workflows interest group to influence future research infrastructure developments. 

Supercomputing access powers paediatric research

Dr Patricia Agudelo-Romero presents a poster at the 2024 AAAI conference (supplied).

Demand for high performance supercomputing resources among life scientists is increasing thanks to consistent growth in both the scale and complexity of omics datasets and analyses. The Australian BioCommons Leadership Share (ABLeS) offers a specifically tailored mix of infrastructure and computational resources to support life sciences research, providing an alternative access mechanism to Tier 1 resources outside of onerous merit-based applications. 

The Kids Research Institute Australia, formerly Telethon Kids Institute, is a great example of the support ABLeS provides to research groups. As a word-class paediatric research centre, The Kids is committed to improving children’s health across its 4 key research themes: Indigenous Health, Brain and Behaviour, Chronic and Severe Diseases, and Early Environment. Many of its programs require sophisticated computational biology tools and resources, including the P4 Respiratory Health for Kids team. The P4 team focuses on the significant healthcare burden of childhood respiratory diseases, with around 20% of Australian children developing recurrent respiratory disorders such as wheezing and asthma.

Dr Patricia Agudelo-Romero, Senior Research Fellow, leads the computational biology and bioinformatics arm of the Wal-yan Respiratory Research Centre within The Kids and is a key member of the P4 team. She uses ABLeS resources to conduct omics analyses including epigenetics, transcriptomics and metagenomics. Patricia and the P4 team recently presented two studies enabled by ABLeS - understanding the methylation landscape of in utero programming in relation to asthma risk factors (part of the AERIAL study), and exploring the complexity of the human respiratory virome. The methylation study was a featured poster at the 2024 American Academy of Allergy, Asthma & Immunology conference, while the lung virome work won best selected talk at the Microbiome Virtual International Forum in 2022, having uncovered a high diversity of bacteriophages in the airways, which may play an important role in modulating the lung ecosystem. 

ABLeS enabled both our studies to process more than 2,300 FASTQ files from targeted high-throughput methylation sequencing and shotgun metagenomics experiments, using two methylation-related nextflow pipelines and one related to virus discovery. These large-scale and computationally demanding analyses would not be possible without cutting-edge resources like our access to the Pawsey Supercomputing Research Centre provided through ABLeS.

In alignment with the open-science principles of ABLeS, Patricia has made her nextflow pipelines publicly available through the nf-core community - namely the EVEREST for viral assembly and characterisation, and target-methylseq-qc which performs downstream analyses after running a standardised nf-core methylseq pipeline. The same nf-core pipeline is being applied in another project at The Kids Institute, where the Clinical Epigenetics team are analysing whether a mediterranean diet induces DNA methylation changes in pregnant women as part of the ORIGINS study. ABLeS is enabling the team to run the methyl-seq pipeline, including ensuring the pipeline can be run on the upcoming Australian Nextflow Seqera Service.

Could your research team benefit from what ABLeS offers? Watch Dr Ziad Al Bkhetan give an overview of the service.

Video tutorial simplifies sharing of bioinformatics tools

Thousands of bioinformatics tools from across the entire omics spectrum are available within Galaxy’s user-friendly web interface. New guidance videos developed by the Galaxy Australia team are supporting anyone with a little bit of coding know-how to add their favourite tools into the global Galaxy platform.

With over 11,000 individual users accessing Galaxy every month, there are frequent requests to add new tools that cater to an ever expanding array of research needs, and there is often a backlog of tools waiting to be ‘wrapped’ for use in Galaxy. The vibrant community of contributors who maintain Galaxy are passionate about open source and accessible science, and invite all tool developers, researchers, and research communities to add bioinformatics tools to Galaxy. 

Galaxy Australia’s Dr Cameron Hyde and Michael Thang have prepared two new videos that explain and demonstrate the tool wrapping process to help anyone prepare tools for  inclusion in Galaxy workflows across the globe.

In part one, Michael introduces the Galaxy platform, explains the process of wrapping tools for Galaxy and describes the tool parameters that can be incorporated into the underlying code (XML). Then in part two, Cameron steps through the process for building an XML wrapper to add a tool to Galaxy using Planemo. To get the most out of the tutorial, you’ll need to have a basic understanding of Linux command line (Bash) and XML syntax, and be comfortable working with a code editor. These videos complement the extensive documentation available in Planemo and the Galaxy Training Network.

If there is a tool missing from your Galaxy workflow, or you’d like to make your own tools available to a global audience, start wrapping with the Getting tools into Galaxy videos!

Bioinformatics innovations helping keep Australia safe from plant-borne disease

The DAFF science and surveillance team (provided).

If you’ve ever watched Border Security, you’ll know that Australia’s unique ecosystem is fiercely protected from incoming plant diseases. The Australian Government’s Department of Agriculture, Fisheries and Forestry (DAFF) is at the frontline of ensuring the safety of plant materials that are commercially imported. With increasing demand for high throughput screening, they leveraged Galaxy Australia to help ensure new diseases don't slip through.

At DAFF’s post entry quarantine facility in Mickleham, viruses and viroids make up two-thirds of all diseases screened for. With import quantities growing, the demand for viral screening was placing an unmanageable workload on DAFF staff using conventional screening methods. Now, a long-standing collaboration between DAFF and A/Prof Roberto Barrero at QUT has produced an innovative bioinformatics workflow for viral screening called VirReport. It employs small RNA sequencing and can be readily deployed on Galaxy Australia and other compute infrastructures. 
As part of the collaboration, the Galaxy Australia team ensured all the necessary tools were available to support the development of a series of virus reporting workflows. DAFF’s Operational Technology team led by Callum Tyle automated the entire process in Galaxy using the public Galaxy API and the BioBlend python library from data upload, job scheduling and monitoring, through to data download. Dr Ruvini Lelwala, Bioinformatician - Operational Science and Surveillance (Post Entry Quarantine Facility) - in DAFF’s Science and Surveillance Group, then got busy training molecular biologists and plant pathologists to use VirReport, to the extent that anyone with training can now easily trigger the screening process. Ruvini speaks highly of the experience working with Galaxy:

The robust and well documented Galaxy APIs have allowed for a tailored experience to be provided to our staff within a dedicated web interface, allowing staff to schedule analyses and view results. The workflows are now routinely used by our bioinformatician and other staff at DAFF.

VirReport has become the primary screening method used by DAFF for imported Prunus (stone fruit), Rubus (brambles), Fragaria (strawberries) and clonal grasses (e.g. Zoysia, Stenotaphrum). Since deployment, 693 samples have been processed through the GA-VirReport workflow. Ruvini highlighted several Galaxy Australia features that the team enjoy:

Recent changes to searching and viewing histories have streamlined our data movement between histories, and the ability to conditionally skip workflow steps ensures continuation of independent processes within a workflow. We’ve also noticed an expanding suite of tools for statistical evaluation and data visualisation, which we continue to explore.

Learn more about the implementation of the Galaxy Australia viral screening workflow in the team’s publication: Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants.

Learn new biological data analysis skills at this free online global training event

The Galaxy Training Network is thrilled to bring you Galaxy Training Academy 2024. This week-long, completely free, global online event will help you master the Galaxy platform for data analysis. This web-based platform is widely used by researchers world wide and gives you access to 1000’s of popular tools for analysis and processing of biological data.

What you learn is entirely up to you - there are learning tracks dedicated to bacterial genomics, genome assembly, machine learning, microbiome analysis, single cell omics, transcriptomics, and viral genome sequencing. Choose what’s of interest, learn at your own pace, and get online support 24/7 through dedicated Slack channels. The Galaxy Australia team will be on hand to answer on Slack when everyone else is asleep!

Don’t miss this opportunity to advance your skills in bioinformatics and data analysis!

When: 7 - 11 October, 2024

Where: Online

Format: Asynchronous, choose-your-own-adventure, video tutorials with online support

Price: Free

More information and registrations via the Galaxy Academy 2024 website.  

Registrations close on 30 September 2024

Australia’s new Nextflow Ambassadors connect users to global community

Nextflow has emerged as a standard for defining bioinformatics workflows. Australian BioCommons is responding to increased use of Nextflow in the life sciences by convening the Bioinformatics Workflows community, offering Nextflow training, and standing up an Australian Nextflow Seqera Service. Now, Australia has two Nextflow Ambassadors to support the researcher community.

Dr Georgie Samaha and Dr Ziad Al Bkhetan have been awarded positions in the Nextflow Ambassador Program to ensure Australian users are represented on the global stage. The program fosters collaboration, knowledge sharing, and community growth. 

Georgie is the bioinformatics group lead of the Sydney Informatics Hub at the University of Sydney and is passionate about making bioinformatics more accessible for researchers. She works with BioCommons to develop public digital infrastructure and leads the BioCommons BioCLI project.

I’m excited to help bridge the gap between life scientists using Nextflow and technical experts. As ambassadors we can understand their needs and voice them directly to Seqera

Ziad is Product Manager, Bioinformatics Platforms at Australian BioCommons and enjoys uplifting life scientists to achieve their research outcomes in two BioCommons services:  ABLeS and the Australian Nextflow Seqera Service. 

I’m looking forward to acting as a local contact for Nextflow users, and helping to build a national Nextflow capability that can contribute best practice workflows to the international community.

Dr Geraldine Van der Auwera, Lead Developer Advocate at Seqera (the company behind Nextflow), is looking forward to meeting the ambassadors in person when she visits Australia in September:

We're thrilled to have Georgie and Ziad join the Nextflow Ambassadors! We're keenly aware of the distance and time-related challenges that exist between Australia and other Nextflow hubs, so we expect that having not one, but two ambassadors available to share their expertise with their local networks will make a big difference! We’re hopeful that their localised support, training, and knowledge sharing will ensure that researchers and institutions across Australia can utilise Nextflow effectively in their work.

Both ambassadors have hit the ground running, with Ziad presenting at the upcoming Nextflow Summit Barcelona 2024, and Georgie playing a key role in organising national training events like the upcoming Hello Nextflow! workshop.

Georgie and Ziad are assessing interest in the formation of an informal Australian Nextflow network that would benefit life scientists, and they want to hear from you! If you use Nextflow, or are planning to in the near future, share your thoughts by filling out this brief survey.

Strengthening ties with European research infrastructures at ELIXIR All Hands

Photo credit: Mikael Wallerstedt

A special seat at an international table was recently reserved for Australian BioCommons to share insights and address the challenges of building and sustaining distributed life science data infrastructure. The invitation to represent Australia’s activities at the 2024 ELIXIR All Hands provided the opportunity to reach more than 500 professionals from over 25 countries. Participants shared their successes and looked to collaboratively address ongoing challenges facing life science research infrastructures.

ELIXIR, as Europe’s life science research infrastructure, has a mission that is closely aligned with that of Australian BioCommons, and we have maintained a collaboration strategy since 2020. With ongoing face to face interactions a key component of the strategy, Australian BioCommons was well represented at the 2024 All Hands meeting with Dr Jeff Christiansen, Dr Tiff Nelson, and Dr Ziad Al Bkhetan all attending in Uppsala, Sweden.

The BioCommons team joined stimulating discussions that addressed key areas in ELIXIR’s scientific vision including cellular and molecular research; biodiversity, food security and pathogen; and human data and translational research. Among these discussions, Ziad presented the Australian Nextflow Seqera Service while Tiff shared our array of infrastructure supporting genomics research in Australia. Tiff was particularly excited by the emerging focus on biodiversity:

As European research data infrastructures’ focus turns to biodiversity, our experience working with Bioplatforms Australia Framework Initiatives like the Threatened Species Initiative and the Amphibian and Reptile Genome Initiative becomes so valuable. We’re looking forward to continued discussions with ELIXIR’s biodiversity community.

Jeff also found great value in making connections with other national infrastructure providers at All Hands 2024, including having the opportunity to also visit the Swedish Node of ELIXIR, National Bioinformatics Infrastructure Sweden (NBIS) at SciLifeLabs in Uppsala to connect on topics of mutual interest.

It was fantastic to renew existing connections and meet international partners like NBIS in person. One highlight was the crossover in our efforts to better support omics data management at a national level, and researchers’ omics data submissions to international repositories.

Read ELIXIR’s summary of the meeting

Galaxy Australia well represented at GCC2024

Last month, Galaxy Australia team members took the rare chance to work alongside over 150 other Galaxy developers in the same time zone at the 2024 Galaxy Community Conference (GCC). With 28 countries represented in Brno, Czech Republic, GCC was the perfect meeting place to celebrate Galaxy’s successes, discuss the latest developments, and work together to improve the Galaxy platform that enables accessible, reproducible, and transparent computational biological research.

Catherine Bromhead (Galaxy Australia Infrastructure Team Lead) presented the latest developments on the Total Perspective Vortex, a job scheduling tool originally developed by the Galaxy Australia team. With even further nuanced controls available, the Aussie Vortex is being adopted by Galaxy services around the globe. 

Gareth Price (Galaxy Australia Project Lead) represented Australian interests at the Directions Summit, co-launched a forum for Galaxy users to have input on the Galaxy Project’s roadmap, and delivered the Australian section of the prestigious ‘State of the Galaxy’ annual talk. In his talk, Gareth explained that:

The Galaxy Australia team maintains a strong community focus when we develop new offerings. We’re particularly proud of delivering on requests for specialised commercially licensed tools and custom workbenches like the Genome Lab.

After four days of presentations and training workshops, the two day Collaboration Festival saw participants work on solutions and enhancements in a way that is only possible when the global team comes together. For Gareth, adapting the Genome Lab code so that it can be repurposed for any other domain across the world was a particular highlight. 

Galaxy Labs are a fantastic entry point for Galaxy users, and the team are excited to make Galaxy Australia even more accessible for a wide range of domain specialists by developing new Galaxy Labs. Stay tuned for new releases soon!

Work on Galaxy Labs will continue as just one of many exciting projects at ELIXIR’s BioHackathon. If you’re interested in a unique opportunity to participate in this significant global event and network with your international peers while working intensively on practical bioinformatics challenges, consider joining the Australian Outpost!

Read the full GCC2024 meeting report at Galaxy News.
If you’d like to keep up with plans for GCC2025, subscribe to the BioCommons newsletter or Galaxy Announcements.

WorkflowHub and nf-core collaboration enhances workflow accessibility

This media release was prepared by ELIXIR-UK with assistance from BioCommons and is re-published here without modification.

WorkflowHub, a prominent registry for computational workflows, now automatically registers workflows developed by nf-core, a community-driven initiative focused on developing best-practice workflows. 

The marriage of these two resources will not only allow new workflows to be included automatically, but also updated versions of existing ones.

Additionally, during the import process, workflows are automatically annotated based on the metadata provided by the nf-core community in their native development repositories. This ensures that the workflows are visible, well-documented and easily understandable, following the principles of FAIR (Findable, Accessible, Interoperable, Reusable) data practices.

Contributions from the nf-core community are now streamlined and automated, freeing up valuable time and resources for both WorkflowHub and nf-core teams to focus on creating high-quality workflows without the added burden of managing findability and accessibility.

Developments in WorkflowHub are steered by the joint Product Owners Prof Carole Goble, ELIXIR-UK, Dr Frederick Coppens, ELIXIR-Belgium, and Dr Johan Gustafsson, Australian BioCommons. Recognising the increasing importance of Nextflow as a standard for defining bioinformatics workflows, the team engaged with nf-core to automatically ingest nf-core workflows to WorkflowHub.

About WorkflowHub

WorkflowHub is a leading registry for computational workflows, providing a platform for discovering, sharing, and using workflows across various scientific domains. It aims to enhance the accessibility and usability of computational workflows, promoting collaboration and innovation in the research community.

About nf-core

Nf-core is a community-driven initiative focused on developing best practice workflows using the Nextflow workflow management system. It provides a platform for collaborative development and sharing of high-quality workflows, fostering reproducibility and efficiency in computational research.

About ELIXIR-UK

ELIXIR-UK is part of the European ELIXIR infrastructure, which supports life science research and its translation to medicine, the environment, and society. By integrating national bioinformatics resources, ELIXIR-UK aims to provide a sustainable infrastructure for biological information, ensuring that data is effectively managed, analysed and shared across the scientific community.

The UK Node, as well as the Belgium Node of ELIXIR, endorse WorkflowHub as a Node Service. 

Further details reach out to us at contact@elixiruknode.org

About BioCommons

Australian BioCommons is a digital infrastructure capability enhancing Australian life sciences research. BioCommons links Australian researchers with the tools, platforms, and expertise they need to undertake world-class research into the molecular basis of life.

BioCommons facilitates links between the Australian research landscape and international platforms and communities, and contributes directly to WorkflowHub’s development and governance. This contribution forms part of an ongoing collaboration strategy between BioCommons and ELIXIR to share technical experience and maintain a more global perspective. 

For further details, reach out to us at comms@biocommons.com.au