New high memory servers for Galaxy Australia

Researchers’ capacity to analyse their life science data was boosted this week when high memory compute servers for Galaxy Australia came online at the University of Melbourne.

Almost 500 researchers from the University of Melbourne and the surrounding precinct already use the Galaxy Australia platform for data integration and analysis. Some of their work regularly challenges the platform by using tools with particularly high memory demands like Mothur, Trinity, Canu and BLAST which were until now unsupported by Galaxy Australia.

The new high memory virtual machines will see researchers pushing new limits and open opportunities to access powerful tools, including those for machine learning, cheminformatic analysis and long read sequencing. The large-capacity and high-performance local storage the new servers provide is itself a new capability that will help accelerate specific types of workloads. Researchers that are currently running particularly high memory tools come from a wide variety of institutions including the Florey Institute of Neuroscience and Mental Health, University of Tasmania and the Royal Botanic Gardens, Victoria. We look forward to sharing examples of specific research projects benefiting from the servers once they are in use.

Galaxy Australia consists of a single head-node site and multiple satellite ‘Pulsar nodes’. The Head node contains all the central infrastructure required to run the Galaxy platform, whereas the Pulsar nodes provide distributed compute to parallelise job requests. User jobs are executed at the Head node or Pulsar nodes based on the combination of dataset size and tool.

As the host of the Australian BioCommons hub and key partner in Galaxy Australia, Melbourne Bioinformatics was perfectly placed to coordinate this significant capital investment from the ARDC into the Melbourne node of the Nectar Research Cloud. 

The Pulsar nodes operated by the University of Melbourne and QCIF have both received support and investment from the Australian Research Data Commons (ARDC) and Australian BioCommons to procure new servers with 2 or 4 terabytes of memory. Two 128 core servers, one with 2 TB and one with 4 TB of  RAM, have been installed on the University of Melbourne node of the ARDC Nectar Research Cloud with the assistance of the University’s Research Computing Services team. The high memory servers for the QCIF Galaxy Pulsar node will be commissioned in the coming months. 

Galaxy Australia team helping to lead a truly global research activity

The successful mature research software infrastructure project that is Galaxy has evolved over many years, and has benefited from the participation of thousands of people around the world. The Galaxy Community is made up of the passionate people who constantly improve and expand on what Galaxy does, plus its diversifying and exponentially growing user base. Responding to the increasing complexity that comes with a rapidly growing audience and to fully engage the international Galaxy Community, a range of new governance structures have been formed. Aussies are well represented in many of these new community groups, reflecting the truly global collaboration and the esteem earned over the years of Galaxy Australia contributions.

The Galaxy Executive Board has members from Europe, USA and Australia, including Andrew Lonie (Director, Galaxy Australia). The Board has drawn together the Global Galaxy Steering Committee to represent community interests and has Ross Lazarus as its Chair and Maria Doyle (Peter MacCallum Cancer Centre) and Simon Gladman (Melbourne Bioinformatics, Galaxy Australia) in its ranks.

Simon’s various roles showcase the complexity of what's required behind the scenes of Galaxy’s sophisticated offering. In addition to participating in the Global Galaxy Steering Committee, he’s a contributor to the Intergalactic Utilities Commission, the Intergalactic (Reference) Data Commission and the Galaxy Training Network. To share his skills with the community he regularly leads Global Admin Training, and also offers local training workshops via Melbourne Bioinformatics and national events via Australian BioCommons. Simon contributes to the Galaxy Admins working group, which is one of a raft of small community-led working groups that manage different aspects of the Galaxy ecosystem.

Growing the Galaxy community in our region, Christina Hall (BioCommons) and Anna Syme (Melbourne Bioinformatics) participate in the Outreach and Training working group, and Christina forms part of the Global Outreach and Communications Committee. 

Simon, Christina and Gareth Price (Galaxy Australia’s Service Manager) helped to organise last year’s international Bioinformatics Community Conference which was a great way to network with Galaxy community members in friendly timezones. The publications from that event can be found at Galaxy’s F1000 Gateway where community members continue to submit their work for peer review by a Galaxy community panel that includes Gareth. Gareth and Simon will again offer their expertise as part of the Organising Committee of the upcoming Global Galaxy Community Conference 2021.

As the capabilities and capacities of Galaxy rapidly grow, the Galaxy community continues to reach out and welcome newcomers, and it is hoped that this new governance framework will enable Galaxy to build its truly global community.

BioCommons supports the creation of specialist training with Genomics for Australian Plants

Australian BioCommons partners broadly in our efforts to drive coordinated solutions to life science researchers’ problems. We connect the appropriate large organisations, small facilities, collaborative initiatives and individual experts to solve community-scale challenges. This means we’re well placed to hear about new resources and help to bring training opportunities to fruition. 

Genomics for Australian Plants (GAP) is developing genomics resources to enhance our understanding of the evolution and conservation of the unique Australian flora. Established in 2018, the Australian State and National Herbaria and Botanic Gardens came together with Bioplatforms Australia to form the GAP initiative that has flourished as an active national consortium of researchers and expert working groups.

One of GAP’s goals is to build capacity in the management and application of genomic data and to provide tools to enable genomic data to be used to identify and classify biodiversity at a range of scales. Bringing together staff from Royal Botanic Gardens Victoria, CSIRO’s Centre for Australian National Biodiversity Research (Canberra) and Australian Tropical Herbarium (Cairns), Bioplatforms Australia and Australian BioCommons, GAP’s phylogenomics-bioinformatics working group has combined newly developed and existing scripts into an integrated workflow for the assembly of target capture data. 

Keen to share these resources with researchers who can use them, the group has been working with BioCommons to offer a series of events to train others in using these novel pipelines. Theoretical webinars and hands-on training workshops will be delivered virtually in conjunction with the upcoming Australasian Systematic Botany Society Conference.

BioCommons offered advice on how to train others in what we’ve built: what was possible to run live, which computational environment would work best and the practicalities of leading a group through hands-on learning exercises. With their support we’ve been able to focus on our strengths like making sure the pipelines, data and technical information are spot on.

- Lalita Simpson, Research Community Project Manager,
Genomics for Australian Plants - Phylogenomics Project.

Introductory overviews of the challenges of conflict within target capture datasets and strategies to employ during analysis will be delivered as short public webinars:

• Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation (20 May)

• Detection of and phasing of hybrid accessions in a target capture dataset (10 June)

For participants who would like to take the next step, a series of three interactive in-depth workshops will be delivered as part of the ASBS conference. The analysing target capture datasets workshops are suited to researchers analysing target capture datasets and will provide hands-on training in the use of workflows covering the processing of raw sequence reads, as well as strategies for resolving paralogy and hybridisation. 

• GAP phylogenomics bioinformatic pipeline – Part 1: Assembly of raw reads using HybPiper (6 July)

• GAP phylogenomics bioinformatic pipeline – Part 2: Yang and Smith paralogy resolution (7 July)

• HybPhaser – Detection and phasing of hybrid accessions in a target capture dataset (8 July)

Further information and registration details are available on the ASBS2021 conference website.

BioCommons bioinformatics training program making great progress

With all the talk about 'hybrid' training these days, we were happy to recently publish our own unique hybrid method that we've used since 2016 in PLoS Computational Biology. Our application of a bioinformatics training delivery method for reaching dispersed and distant trainees is a practical 'how-to' description of the method we developed over the years to make our hands-on training easily accessible to a national audience. Pivoting to completely online training in 2020, we engaged 363 registrants in 8 workshops and recorded 17 webinars which have clocked up over 6000 views. We're about to hit 1,000 subscribers on our YouTube channel too.

All of our training activities are made possible by the participation of a raft of enthusiastic volunteers from around Australia and beyond. The list grows with every event, and you can see the huge amount of goodwill in our community from the many names and affiliations on our trainers page.

The enthusiasm that we and our partners have for sharing training resources and opportunities has inspired us to form the Bioinformatics Training Cooperative. We've begun offering collaborative workshops that are open to anyone in Australia - connecting researchers directly with expert trainers they wouldn't normally have access to. Via the co-op we have recently worked with Melbourne Bioinformatics and Pawsey Supercomputing Centre to offer a multi-day workshops on both RNA-Seq analysis and using containers in bioinformatics', and next up we're bringing a series of workshops in variant calling in viruses, bacteria and eukaryotes led by QCIF.

If you think your organisation could contribute to the Bioinformatics Training Cooperative please let us know. 

Keep up to date with new collaborative training opportunities as soon as they are announced by following @AusBioCommons on Twitter or subscribing to our monthly newsletter.

Better plant quarantine enabled by Galaxy Australia’s two millionth job

Plants grown at the Post Entry Quarantine facility in Mickleham, Victoria (Photo: Robin Eichner, DAWE)

To celebrate the broad uptake and diversity of their users, Galaxy Australia took the opportunity to spotlight the researcher who submitted the two millionth job to the service. 

Dr Ruvini Lelwala is a Bioinformatics Research Associate at the Queensland University of Technology (QUT). However Ruvini is based at the other end of the country at the Post Entry Quarantine (PEQ) Facility in Mickleham, Victoria, which importantly places her where high-risk plant material undergoes quarantine after importation into Australia. 

Working within a multidisciplinary group of bioinformaticians, computational biologists, molecular biologists, plant pathologists and policy makers, Ruvini’s PhD in plant pathology is put to good use as the team develops enhanced diagnostics for the detection of exotic plant pathogens.

Under the guidance of A/Prof Roberto Barrero, eResearch Office (QUT), Ruvini and bioinformatician Dr Marie-Emilie Gauthier work closely with the Australian Department of Agriculture, Water and the Environment (DAWE) Science and Surveillance Group at PEQ while liaising with a wider community from QUT, DAWE, Agriculture Victoria, Hort Innovation and New Zealand Ministry for Primary Industries.

Roberto’s team has developed a novel bioinformatics toolkit – Virus and Viroid Surveillance and Diagnosis (VSD) toolkit, which can be used to detect viruses and viroids from host plant RNA extracts. High Throughput Sequencing (HTS) enables the rapid detection of viruses and viroids in imported plant material in a single test and can accelerate the release of plant genetic stocks held at PEQ facilities. 

eResearch@QUT provides access to research tools and end-to-end analytical workflows that run on diverse compute resources, enabling reproducible large-scale processing of plant biosecurity samples. The team also partners with Galaxy Australia to provide a bioinformatics training interface for staff at PEQ.

Galaxy Australia is useful in the development and implementation of their VSD pipeline through creating dataset collections, databases, automated workflows, quality control of sequencing reads, targeted genome assembly, finding open reading frames, and sequence similarity searches, amongst other tasks. 

I can seamlessly submit multiple jobs to Galaxy Australia that can be queued and run in parallel on multiple ‘histories’. Moreover, there’s a good support team if I ever need help with troubleshooting.

Dr Ruvini Lelwala, QUT

The Galaxy Australia ‘tool shed’ already has the majority tools needed, but Ruvini simply requests that new ones are added as required. Galaxy Australia is an active contributor to the global repository of analytical tools and encourages its users to explore the potential of over 8,000 tools to boost their analytical options.

Ultimately they aim to recreate the VSD pipeline on Galaxy Australia, implement the pipeline in real-time and train PEQ molecular biologists to use the pipeline to process and analyse HTS datasets. Galaxy Australia enables the team to provide access to specialised plant viruses/viroids diagnosis pipelines to their collaborators who do not have formal training in bioinformatics. The platform helps upskill molecular biologists thanks to its user-friendly Graphical User Interface and the availability of supportive training materials. 

The long-term goal is to use Galaxy Australia to facilitate routine quarantine testing of imported plants using HTS technologies. The potential impact on Australia's horticulture sector of faster access to new plant stock has been documented previously in QUT’s Using next generation genetic testing to give growers a competitive boost.   

The two projects using Galaxy Australia are:

MT18005 ‘Improving access to new germplasm through faster and more accurate diagnostics’ funded by Hort Innovation using the Hort Innovation Citrus, Grape Tables, Rubus, Potato and Nursery research and development levy, co-investment from Queensland University of Technology and contributions from the Australian Government. Hort Innovation is the grower-owned, not-for-profit research and development corporation for Australian horticulture.  

BIP202048 ‘Transformation of exotic plant disease testing at PEQ, Mickleham by implementation of high-throughput sequencing’, is funded by the Department of Agriculture, Water and the Environment (DAWE) Biosecurity Innovation Program. 

For further information contact:
A/Prof. Roberto Barrero
eResearch Office, Queensland University of Technology
roberto.barrero@qut.edu.au

Find the tools, workflows and compute you need

We all know that finding the right computational tools for your research can be frustrating. Which tools do what, where can you find them and which high end computers can you access?

Australian BioCommons has worked with their infrastructure partners to pull together a convenient list of the tools, workflows and compute systems that are available to Australian life science researchers. The new searchable pages offer a landscape view of what’s out there, providing a quick scan of available high performance computing resources, local installations of bioinformatics tools and useful details about relevant workflows. Click below and watch with sound or captions for a quick tour.

The Australian BioCommons Technical Documentation pages open up information that is often scattered and opaque. The birds-eye-view of the national research infrastructure ecosystem will be useful for the whole range of researchers from the uninitiated biologist to the bioinformatician seeking targeted technical specs. The lists are not exhaustive and will grow over time - you might like to add your own resources to make them more findable by your peers!

It will make our life easier to know where and how to access the resources we need. 

Mike Thang, Bioinformatician 
Institute for Molecular Bioscience, University of Queensland

From ABRicate through to zsdt, you can currently find the details of 400+ tools and workflows. Already know the particular tool you need for your analysis? You can search the tool’s availability and find which versions are installed at various facilities. Maybe you can get what you need without going through a formal allocation process, or discover some new tools by searching by topics like sequence alignment or phylogenomics.

The tools list will be a really useful resource for researchers, particularly those who are just getting started and want to understand what software is available for their analysis and what computing platform would be most suitable. It’s awesome to have all of that information on hand in the one place! 

Parice Brandies, PhD Candidate
School of Life and Environmental Sciences, The University of Sydney

Visit the new listings of tools, workflows and compute systems available across Australian BioCommons partners at the Australian BioCommons Technical Documentation pages.

Record setting global Galaxy training event

The largest-ever Galaxy training event, “GTN Smörgåsbord: a global Galaxy course” was run last month. It attracted 1189 registrations from 76 different countries, and engaged 583 live on Slack (chat platform).  The event was completely asynchronous, meaning that all training materials - pre-recorded videos, slides, hands-on manuals, and the compute to run tutorials - were available online at any time people wanted to participate.

Over 60 instructors volunteered to be available on Slack throughout the week to answer questions. Several Galaxy Australia and Australian BioCommons team members made themselves available, and combined with instructors across the world, continuous support was available for anyone who needed it regardless of their location.

This course was made possible through the support of the 3 largest Galaxy servers, Galaxy Main (US), Galaxy Europe, and Galaxy Australia. The teams behind each of those Galaxy servers invested a lot of time and effort to ensure all necessary tools were available and running smoothly, and that sufficient resources were available to handle such a large number of participants at the same time. Given the computational load was spread over multiple sites participants could use the server nearest them for the best experience.

Originally planned as a small 20 person European workshop, then an online course when the pandemic struck, Galaxy Australia offered to co-host the event in order to make it more accessible to researchers in our time zone. Thankfully the generous Galaxy community responded with “Sure! We’ll open this up to everyone!”. We joined with instructors and organisers from the CINECA project, the Gallantries, and the worldwide Galaxy community to offer this amazing global, 24/7 training event covering all time zones.

The event was deployed using the same innovations tested for the 2021 Galaxy Admin Training course. This global event for 88 participants was rolled out online for the first time in January using methods described in a recent Gallentries blog post. 

The feedback from participants (and instructors) of the Smörgåsbord was excellent and there are calls to do it again. You can view the collection of 43 video tutorials created for the training event that cover a diverse sample of the Galaxy Training Network materials. 

The feedback from participants (and instructors) was excellent and there are calls to do it again. You can view the collection of 43 video tutorials created for the training event that cover a diverse sample of the Galaxy Training Network materials. 

The Galaxy Project YouTube channel also has snackable videos that share how to get involved in the Galaxy Community and what the Galaxy Training Network has to offer. You’ll also find short narrated introductions to the Galaxy interface and a variety of Galaxy functionalities, as well as longer webinars to introduce new advanced features.

For further information, there’s a comprehensive summary of the GTN Smörgåsbord: a global Galaxy course written by the organisers on the Gallentries blog.

New Human Genome Informatics Lead

Australian BioCommons recently welcomed A/ Prof Bernie Pope to the role of Associate Director: Human Genome Informatics. Bernie is a Victorian Health and Medical Research Fellow, based at Melbourne Bioinformatics, The University of Melbourne. His research focuses on applying computational techniques to biological questions, especially related to human genomics and cancer. Bernie is also a passionate educator and has extensive experience teaching at the university level.

Bernie is well known in the research community, having spent years collaborating as PI on many high profile national and international cancer projects while also teaching and undertaking his Fellowship, Translating genomics-driven bioinformatics into improved prevention and treatment of colorectal cancer. You may have seen him at the ABACBS 2020 Conference presenting Best practices for bioinformatics command-line software with Bionitio. You can watch Bernie talk about his latest tool in the BioCommons webinar, Bioinitio: building better bioinformatics tools.

Bernie's arrival marks an exciting new era for BioCommons, with the launch of two new Human Genome Informatics projects. We've had online kick off meetings for projects to establish the Gen3 Data sharing platform in Australia and to explore and deploy a raft of other global technologies and standards to improve the sharing of human genomics data for research in Australia.

We're excited to bring together a range of partners including ARDC, ZERO, AGHA, UMCCR, Garvan, QIMR-Berghofer and others, multiple infrastructure partners (including AAF, NCI, AARNet and others), as well as expert international groups (including GA4GH, the developers of Gen3, the ELIXIR Federated Human Data Community, Children’s Hospital of Philadelphia D3b, Seven Bridges Genomics and others) to help ensure that infrastructure for responsible human genome data warehousing, sharing and analysis is implemented in Australia that adheres to various global best practice standards.

Building better genome browsers

We were pleased to see one of our close partners recently awarded a grant to extend on a highly collaborative BioCommons project. Dominique Gorse from QCIF, along with Sandie Degnan and Bernie Degnan from the School of Biological Sciences at UQ, received support for Developing a scalable genome browser and interactive repository for large and complex multi-omic datasets from non-model organisms of environmental and economic importance.

Great Barrier Reef, Queensland (Image: Daniel Pelaez Duque)

Announced as a 2021 UQ Genome Informatics Hub (GIH) collaborative project, it will deliver an interactive repository for diverse transcriptomic, chromatin-state and proteomic data and will be immediately populated with existing genomes of two Great Barrier Reef animals: the notorious destroyer of coral reefs, the crown-of-thorns starfish and a model for animal evolution, the sponge Amphimedon queenslandica”. 

QCIF are a key contributor to BioCommons activities around developing systems for non-model organism de novo genome assembly and annotation, and will launch a new national hosted Apollo service as part of that initiative in coming months. In the GIH project the Apollo browser and service will be extended to provide an interactive repository facilitating the viewing and interrogation of a wide range of omics data used for the curation and annotation of non-model organisms.

The GIH is an initiative designed to develop and advance innovative genomic capabilities at the University of Queensland. To find out more about their activities, visit the recently launched a website and subscribe to their newsletter.

Chan Zuckerberg Initiative injects funds into Galaxy platform for biomedical research

This ARDC news story is republished with permission

The global Galaxy Project has been awarded a US$190,000 grant by the Chan Zuckerberg Initiative (CZI) to extend Galaxy—a web-based computational platform—so that it can analyse large biomedical datasets and integrate with other analysis tools.

Galaxy is a free, web-accessible, open-source research platform that life scientists can use to test, evaluate and peer review their work. Used by hundreds of thousands of scientists across the world to analyse biomedical data—including genomic, proteomic (the study of proteins produced by genes), image processing, and systems biology data—it has the advantage that users don’t need training in programming or IT to be able to use it to analyse data.

The grant will be used to

• extend Galaxy to allow easy browsing and importing of datasets from large data repositories

• enable Galaxy to efficiently use cloud computing resources for large-scale, near-data computing

• extend Galaxy integration with other data science environments.

The software extension in this project will help solidify the Kubernetes-based version of Galaxy as a full-featured, robust solution for deploying a scalable version of Galaxy on any computing platform, from laptop to computing cluster to a commercial computing cloud. The project will benefit many life science researchers and ensure the further expansion of the global Galaxy community.

This work and the Australian Research Containers Orchestration Service (ARCOS) project, which is a national collaboration being led by the Australian Research Data Commons (ARDC), will help Galaxy Australia more easily deploy new versions of the software across a variety of computational infrastructure.

In 2020, Galaxy Australia was actively part of the international Galaxy platform that responded to the urgent need for insight into the SARS-CoV-2 virus, building a truly global, democratised, reproducible and transparent approach to systematically analysing the virus.
The grant has been awarded to partners at the Oregon Health & Sciences University, Johns Hopkins University and Melbourne Bioinformatics at the University of Melbourne. Associate Professor Andrew Lonie, Australian BioCommons Director and Senior Advisor at Melbourne Bioinformatics is very pleased to hear this news.

“This team has been working together for some years now, first building the Genomics Virtual Laboratory and more recently developing features for Galaxy to function better in distributed and cloud computing environments. This project grant acknowledges, formalises and strengthens this collaboration, enabling more coordinated efforts and, through that work, better infrastructure for our life science researchers,” said Andrew.

Galaxy Australia is now a mature, life science data analysis infrastructure and service. It has been funded over many years by National Collaborative Research Infrastructure Strategy (NCRIS) initiatives. It is hosted, co-funded and driven by Galaxy project teams at Melbourne and Queensland Universities (Melbourne Bioinformatics and Queensland Cyber Infrastructure Foundation). Ongoing support also comes from ARDC’s Platforms program and Nectar Research Cloud, Australian BioCommons, Bioplatforms Australia, and Pawsey Supercomputing Centre and from Queensland Government's Research Infrastructure Co-investment Fund.

The Chan Zuckerberg Initiative makes grants to organisations working in support of its missions in science, education, and justice & opportunity. Since its launch in 2015, it has awarded about US$2 billion in grants.

For more information read the ARDC story here.

Read the previous Melbourne Bioinformatics announcement here.