Virus research tips Galaxy Australia over 3 million jobs

The Galaxy Australia service is being chosen by large numbers of researchers from around Australia to complete their bioinformatics analyses. Rapid uptake of the service has seen millions of jobs submitted across a broad spectrum of critical research questions with hard-hitting outcomes for the real world.

Here we highlight the work of Dr Rhys Parry, who recently submitted the three millionth job to Galaxy Australia. Rhys uses Galaxy Australia extensively in his current role as a Postdoctoral Research Fellow in Professor Alexander Khromykh’s RNA Virology Lab in the School of Chemistry and Molecular Biosciences, University of Queensland.

Currently utilising Galaxy Australia for RNA-Seq analysis and assembly of SARS-CoV-2 genomes, Rhys has become a power user since he was first encouraged by his PhD supervisor, Professor Sassan Asgari, School of Biological Sciences, University of Queensland, to make use of Galaxy and the Galaxy training resources.

The Aedes aegypti (top) and Aedes albopictus mosquitoes (below) vector many pathogenic viruses to humans, but non-human viruses remain elusive. Bioinformatics tools from Galaxy Australia helped explore the virome of these mosquitoes. (Picture of mosquitoes by Ana L. Ramírez.)

For my PhD project I assembled close to 4000 RNA-Seq datasets from samples from all over the world - a task that would have been impossible without Galaxy Australia
— Rhys Parry

On the hunt for mosquito-borne viruses, Rhys undertook ‘Trinity’ de novo assembly of the transcriptomes of two medically important mosquito species, Aedes aegypti, the yellow fever mosquito and Aedes albopictus, the Asian tiger mosquito. These two mosquitoes vector significant viruses including Dengue, Zika and Yellow fever. The research not only improved our understanding of the microbiome and virome of these mosquito species, but discovered many novel viruses including one that was pathogenic to humans.

Recognising the value of Galaxy Australia beyond virus discovery and transcriptome assembly, Rhys has also used Galaxy for bacterial de novo assembly and RNA-Seq pipelines and annotation and small RNA mapping and analysis. 

For the past few years, my bioinformatics analyses have used Galaxy Australia extensively to avoid the expense of proprietary software and to allow for reproducible and modular pipelines
— Rhys Parry

Six publications resulting from this work have acknowledged the Galaxy Australia team for not only the maintenance and provision of essential computational resources, but also for the technical assistance and scientific advice that individual team members Dr Gareth Price and Dr Igor Makunin provide users of the Galaxy Australia service.

Parry, R., James, M. E., & Asgari, S. (2021). Uncovering the Worldwide Diversity and Evolution of the Virome of the Mosquitoes Aedes aegypti and Aedes albopictus. Microorganisms, 9(8), 1653. https://doi.org/10.3390/microorganisms9081653 

 Madhav, M., Parry, R., Morgan, J. A., James, P., & Asgari, S. (2020). Wolbachia endosymbiont of the horn fly (Haematobia irritans irritans): a Supergroup A strain with multiple horizontally acquired cytoplasmic incompatibility genes. Applied and environmental microbiology, 86(6), e02589-19. https://doi.org/10.1128/aem.02589-19 

Parry, R., Wille, M., Turnbull, O. M., Geoghegan, J. L., & Holmes, E. C. (2020). Divergent influenza-like viruses of amphibians and fish support an ancient evolutionary association. Viruses, 12(9), 1042. https://doi.org/10.3390/v12091042 

Bishop, C., Parry, R., & Asgari, S. (2020). Effect of Wolbachia wAlbB on a positive-sense RNA negev-like virus: A novel virus persistently infecting Aedes albopictus mosquitoes and cells. Journal of General Virology, 101(2), 216-225. https://doi.org/10.1099/jgv.0.001361 

Parry, R., Naccache, F., Ndiaye, E. H., Fall, G., Castelli, I., Lühken, R., ... & Becker, S. C. (2020). Identification and RNAi profile of a novel iflavirus infecting Senegalese Aedes vexans arabiensis mosquitoes. Viruses, 12(4), 440. https://doi.org/10.3390/v12040440 

Parry, R., & Asgari, S. (2019). Discovery of novel crustacean and cephalopod flaviviruses: insights into the evolution and circulation of flaviviruses between marine invertebrate and vertebrate hosts. Journal of virology, 93(14), e00432-19. https://doi.org/10.1128/JVI.00432-19

Some research presented here received funding through ARC grants DP190102048 and DP150101782 and a University of Queensland PhD scholarship.

Leveraging Galaxy Australia to teach proteomics

The complete set of proteins expressed by a living organism is known as its proteome. Studying the proteome is vital to being able to understand the role of proteins within an organism and how they react to changes in their environment. It can include evaluating how changes might relate to outcomes like a particular condition, disease, or pharmaceutical treatment. The study of proteomes - proteomics - involves the analysis of all proteins, including their composition, structure, modifications, location and functions. Heavily reliant on mass spectrometry, proprietary software is commonly used to turn output data into valuable insights. This can be an impediment for newcomers, who need well designed training materials that are simple and specific for the software they will use in the lab once they learn proteomics techniques and tools. 

Dr Matt Padula from the University of Technology Sydney (UTS), is a Senior Lecturer at their School of Life Sciences, and Director of the UTS Proteomics Core Facility, a facility responsible for providing the technical support and instrumentation to study proteomics. At the recent Biocommons showcase, Dr Padula shared his experience using Galaxy Australia and how it simplifies how he teaches proteomics.   

‘When it comes to actually training students in proteomics you have to develop a whole lot of materials that are specific for certain pipelines and then along comes Galaxy… Galaxy has made life a little bit simpler’ – Matt

There are a number of difficulties when it comes to teaching students proteomics. Firstly, access to proprietary software is a real problem when teaching large numbers of students. To add to the challenge, many university desktops aren’t powerful enough to run the programs smoothly, often resulting in analyses taking several days. To tackle these challenges, Matt turned to MaxQuant - an open source proteomics software designed to analyse large mass spectrometric data sets. While it requires no proprietary licence, MaxQuant’s desktop version still takes considerable time to process, while also being complicated with the setting of different searches and parameters proved problematic for students.

Matt began using MaxQuant through Galaxy Australia because it removes the need for a super powerful desktop and potentially messy software installations, simplifies analysis, and can be run from anywhere, allowing for easier remote learning and access. When using the tool through Galaxy Australia, your hard drive isn’t filled with unnecessary input or output files, and workflow creations are able to continue well into the night without interruption.

For Matt, choosing to use MaxQuant for his analysis and teachings has taken the complexity out of setting up searches, and the abundance of training materials on offer means he can simply direct students over to the Galaxy Training Network website. The tutorials have come in handy for both Matt and his students:

‘I use the excellent online Galaxy tutorials to guide me in the creation of a workflow, which I can just save and call it up when I need it’ - Matt

Matt also made use of Galaxy’s new internal Training Infrastructure as a Service (TIaaS). Providing Matt with clear and live insights into the progress of concurrent tasks, it facilitated tailored support of individual students. TIaaS also allowed the administrators of Galaxy Australia to anonymously monitor the training event and fine-tune any resourcing required to provide the students with the best experience possible. The service will soon be rolled out for use by anyone interested in using Galaxy Australia for their training. 

In addition to providing tools, workflows and training infrastructure, Galaxy also comes with an active community. For proteomics, the Galaxy-P community supports a multi-omics platform that provides integrative analysis and promotes collaboration. The supportive communities are made up of global partners with diverse backgrounds and perspectives, who are extremely passionate about open-source research. They are crucial in creating a supportive and engaging environment that stimulates research and encourages training opportunities for its members. Learn more about Galaxy’s proteomics community or take advantage of the proteomics training materials on the Galaxy Training Network.

Dr Matt Padula at University of Technology Sydney

Local impact through international engagement with ELIXIR

Collaborative activities between Australian BioCommons and ELIXIR have expanded rapidly since the signing of the three year ELIXIR - Australian BioCommons Collaboration Strategy in 2020 to leverage the international synergies between the two research infrastructures. The interactions so far have been productive, friendly and insightful, and span an impressive breadth and depth of topics.

An active diary of BioCommons’ engagements with ELIXIR tracks progress and enhances connections between activities. BioCommons is now participating in a raft of international ELIXIR activities through our national network of partners, involving team members from Bioplatforms Australia, Pawsey, NCI, QCIF, SIH at the University of Sydney and Melbourne Bioinformatics at the University of Melbourne.

Collaboration takes place across a range of ELIXIR Platforms and Australian representation in ELIXIR Communities helps to develop standards, services and training within specific life science domains in both Europe and in Australia. From recurring fortnightly meetings of large communities, to spontaneous targeted discussions to exchange practical updates between individuals, the mode of interactions are as diverse as the topics. Here we cover just a few examples. 

Tools Platform and WorkflowHub Community

The ELIXIR Tool Platform helps researchers find and use computational tools by ensuring that they are properly described, packaged, benchmarked and included in an online registry with links to appropriate documentation and training. Connected to the work of the Tools Platform is WorkflowHub: a registry for scientific computational workflows. Like bio.tools, WorkflowHub promotes FAIR sharing. 

BioCommons is taking a leading role in these activities by integrating with the Tools Platform, establishing solutions to streamline deployment of tools and workflows, and assessing approaches for benchmarking. BioCommons now also offers ToolFinder and WorkflowFinder which integrates directly with bio.tools and WorkflowHub respectively. The community can access these services to discover what bioinformatics tools are available on Australian infrastructures, along with the workflows that have been designed by the BioCommons & its partners and tested on these same infrastructures. 

Sustainability of services underpins these activities as highlighted by a lively, BioCommons-ELIXIR jointly-convened Knowledge-sharing workshop on the design and operation of national- and international-scale bioinformatics services at this year’s ELIXIR All Hands meeting.  

Training 

Training is a core element of enabling scientists to use tools and services to achieve their best research. The BioCommons Training Team and the ELIXIR Training Platform have much shared experience in this area. Meeting regularly to swap ideas and identify common training needs, we collaborate to bring training opportunities to Australian and European audiences (time zones permitting!). ELIXIR Training Platform members are represented on the BioCommons Training Advisory Group, and BioCommons also participates in the development of methods and best practice for sharing (FAIR) training materials. Our close connections have recently supported the creation of a new national registry of training events, materials and trainers for the Australian eResearch community, DReSA which is in turn feeding back into the development of ELIXIR’s TeSS Training Portal. 

Galaxy 

Galaxy is an international, community driven effort to make it easier for biologists to analyse their data without the need for programming skills. There are long established ties and connections between the Galaxy EU, US and AU communities who constantly improve the Galaxy platform by developing and sharing new tools, workflows and training.

Over the past two years the global Galaxy community has worked together to develop and deliver truly international and interactive training events. The GTN Smörgåsbord: a global Galaxy course and SARS-CoV-2 Data Analysis and Monitoring workshop have simultaneously trained thousands of researchers across the world and exemplify the collaborative nature of the Galaxy community.

BioCommons team members attend the regular ELIXIR Galaxy community meetings, sit on the Galaxy Executive Board and other governing committees as well as maintain the very popular Galaxy Australia service.

Whether through technical deep dives and the sharing of expertise, or providing alternate use cases and unique perspectives, the ability to connect directly with ELIXIR members is levelling up BioCommons’ impact and is having a positive influence on the direction and outcomes of many ELIXIR projects. If you would like to meet some of our ELIXIR peers who are actively involved in BioCommons collaborations, please join us for their presentations at the BioCommons Showcase 2021.

Another global training success with the ‘SARS-CoV-2 Data Analysis and Monitoring’ workshop

Australian researchers recently took part in the international workshop, SARS-CoV-2 Data Analysis and Monitoring with Galaxy, thanks to the support of the Galaxy Australia team. 

Joining 750 registrants from 82 countries, local researchers participated in four days of training in SARS-CoV-2 data analysis and data management. Experts from Africa, Europe, the USA and Australia came together to offer 25 tutorials, 7 hours of pre-recorded videos (including lectures, demos and hands-on) and 6 hours of live Q&A sessions. 

Australian experts from QCIF, Melbourne Bioinformatics and Australian BioCommons volunteered to offer live assistance to attendees in our time zone. This opened up the possibility of supported asynchronous participation during our waking hours, with the option of tuning in to daily synchronous Q&A sessions, during which Australian attendees joined the rest of the community as it addressed questions from the international audience. Eighteen people took part from Australia, sharing the experience with a diverse array of students, clinicians, technicians, and senior researchers. During the workshop, the videos had 3200 views, with a total of 320 hours of watch time.

As with all Galaxy community events, this workshop fostered the principles of open data, open science and open infrastructure, which are also key aspects in the global public health challenges brought on by the pandemic. True to that philosophy, all the tutorials are now freely available in the Galaxy Training Network (GTN) and the recordings on the Galaxy Project YouTube channel.

The feedback from participants has been very positive and there are plans to offer the workshop again. Galaxy Australia regularly provides live support to asynchronous Galaxy workshops on a variety of topics, allowing their reach to become truly global. Why not join in next time? These training events are freely available to registrants anywhere in the world, with the materials shared publicly afterwards.

We are so appreciative of the worldwide community of instructors and helpers that make these massive global training opportunities possible!

Head to the Galaxy Europe blog if you would like to read the full report on the workshop outcomes. 

What to do when your bioinformatics outgrows your compute

Need to take your bioinformatics to the next level? Maybe you need to better understand the compute requirements for your bioinformatics workflows, or learn how to access compute that suits your needs as an Australian researcher?

You can now watch the recordings of the popular webinars 'Where to go when your bioinformatics outgrows your compute' and 'High performance bioinformatics: submitting your best NCMAS application' and consult the associated 'cheat sheet' to identify your next steps.

In time for the opening of applications for the National Computational Merit Allocation Scheme 2022, we partnered with Sydney Informatics Hub (SIH) to offer advice to help researchers find the compute their research needs. SIH were already offering tailored support to their University of Sydney researcher community, and were keen to share their expertise more broadly. We drew in our national research infrastructure provider partners to share tips on accessing compute including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey.

You can watch the recording of Where to go when your bioinformatics outgrows your compute and consult the accompanying list of Australian research computing contacts. This ‘cheat sheet’ has been uploaded along with all of the other files, materials and metadata to the Australian BioCommons Training Materials repository.

If you know you need specialised compute infrastructure to support your use of efficient, scalable workflows for your data intensive research, then the High performance bioinformatics: submitting your best NCMAS application webinar provides life science researchers with insights into what makes a strong NCMAS application. It focuses on the technical assessment, and how to design and present effective and efficient bioinformatic workflows for the various national compute facilities.

If you would like to read the supporting documents or attend an online information session about the National Computational Merit Allocation Scheme 2022 round, visit this NCI Help page.

New high memory computers fast-track insights into large genomes

Photo by Rod Long on Unsplash

Galaxy Australia’s new high memory servers have delivered an impressive leap forward for scientists with large datasets and computationally-intensive analyses. In a promising test of new infrastructure capacity, the genome of Australia’s national floral emblem, the Golden Wattle (Acacia pycnantha) was assembled this month on Galaxy Australia, demonstrating game-changing efficiency for the service.

To complete this massive task seamlessly in less than 24 hours vindicates the recent expansion to the data integration and analysis possibilities of the Galaxy Australia platform. The assembly tool, FLYE, was used to process 50GB of raw nanopore data - representing approximately one billion base pairs from the whole Acacia genome. 

Large and complex in comparison to something like a microbial genome, the plant genome was an ideal candidate to test previous limits. This type of analysis could take months using conventional institutional compute resources, and worse still, the job can sometimes be prone to failing at the end of the long processing time. Due to memory limitations, this type of analysis wasn’t previously supported by Galaxy Australia. 

The capacity upgrade came after capital investment from the Australian Research Data Commons (ARDC) and Australian BioCommons was made into the Melbourne node of the ARDC Nectar Research Cloud at the University of Melbourne. An equivalent investment into high memory servers at Galaxy Australia’s QCIF node will also come online this year.

Rapid genome assembly not only increases research productivity, but it also facilitates iterative pipeline optimisation and increases the opportunity to gain more insights quickly. Research becomes more reproducible when it’s possible to update an analysis with a new tool version, or tweak and repeat analyses at the request of a research partner or reviewer.

The tests were performed using unique and valuable data that has been years in the making. Researchers at the Royal Botanic Gardens Victoria have been compiling a Golden Wattle reference genome as part of a national consortium tasked with generating whole genome sequences of iconic Australian flora and fauna. Genomics for Australian Plants was initiated by Bioplatforms Australia in partnership with researchers from the Australian State and National Herbaria and Botanic Gardens, and will ultimately ensure that the Golden Wattle genome is sequenced, assembled and shared. 

David Cantrill, Executive Director Science, Royal Botanic Gardens Victoria, said, 

The genome of Golden Wattle will help us identify which genes are important using comparative genomics for Acacia species of conservation concern, and will boost biogeographic studies on widespread species. We want to identify the genes affecting traits of economic significance such as bioactive compounds or salinity resistance.

The testing of the new Galaxy Australia capability is just the beginning of a comprehensive program of work to ensure all researchers can utilise the new powerful machines. Running whole pipelines that include quality testing of input data, trying different tool usage on data subsets and submitting jobs with a range of different parameters will keep the Galaxy Australia team busy for some weeks. Testing various tools on other big data sets and optimising workflows will ensure that researchers around the country can soon bring their own large genomes and assemble them like never before.

The ARDC and Bioplatforms Australia are enabled by the Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS)

Australian user community growth and infrastructure developments highlighted at global Galaxy conference

The Galaxy Australia team has just returned from the Global Galaxy Conference (GCC) - held virtually again this year - where they joined scientists, administrators and developers from more than 55 countries to share knowledge, skills and expertise in the two-week collaboration fest, training event and conference.

Simon Gladman and Gareth Price represented Galaxy Australia on the GCC Organising Committee and the team was well represented amongst the delegates. The team took the opportunity to highlight the rapid growth of the Galaxy Australia service with talks and posters featuring stories of how Galaxy Australia is responding to community needs and supporting skills development via the integration of new tools and workflows, especially those associated with large genomic data sets. They also took the community behind the scenes to see how recent infrastructure changes, including the move to AARNet and integration with CloudStor, are supporting the growth in demand for Galaxy Australia services, improving data transfer and allowing planning for the long term sustainability and reliability of the service. 

Training was also a highlight of the event with the Galaxy Australia team supporting those in Australian time zones to join the global training event and leading training in the admin track. Of course, the Galaxy Australia team itself continues to grow and the conference was a fantastic opportunity for newer team members Cameron Hyde (USC/QCIF), Grace Hall (Melbourne Bioinformatics), Madeline Basetti (QCIF) to undertake training to increase capacity and capabilities for Galaxy Australia.

Take a look at this blog post for highlights, recordings and training materials from the GCC.

Galaxy Australia course at University of Cambridge

Biologists and wet-lab scientists from the University of Cambridge have just completed a two day introduction to next-generation sequencing taught by Dr Gareth Price. As the Service Manager of Galaxy Australia, Gareth was once again invited to lead the online live subject ‘Next Generation Sequencing Platforms and Bioinformatics Analysis’ from his home base at QCIF.

Postgraduate students and staff from the Department of Genetics at the University of Cambridge were introduced to next generation sequencing technologies (NGS) and how they work, providers, common bioinformatics workflows, standardised file types, and sequence data quality control. They used the open, web-based platform for data-intensive life science research - Galaxy - that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses. The hands-on practicals in Galaxy explored sequencing quality control, before and after removal of low quality samples and concluded with how this data pipes into gene expression studies, variant calling and genome assemblies.

Gareth enjoys helping the graduate students, postdocs and staff members from the University of Cambridge who attend the course, and it’s the second time he has been invited to share his knowledge with a class of 30 students. Participation in global events by the Galaxy Australia team is rapidly increasing as borders become less of an impediment to international scientific projects. The majority of Gareth’s time is spent enabling life science research at many university departments around Australia by training and supporting bioscientists in their use of Galaxy Australia.

For further information about this University of Cambridge bioinformatics training event, read the Next Generation Sequencing Platforms and Bioinformatics Analysis description.

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.