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

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.

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.

CloudStor integration for Galaxy Australia is now live

This latest news from AARNet appears on the AARNet news blog.

Life sciences researchers using the Galaxy Australia analysis platform can now easily and securely move their data to and from the AARNet CloudStor research data storage platform.

This new integration is helping to streamline workflows for Australian researchers collaborating nationally and internationally on projects across the sciences and humanities that aim to solve some of the biggest problems facing our planet.

Galaxy Australia is a vital informatics virtual lab that is allowing researchers to analyse biological data without any specialised knowledge of programming or IT. All the computational infrastructure and software the researchers need is set up and ready to go, simplifying the analysis process for thousands of life scientists. It is operated by the Queensland Cyber Infrastructure Foundation and the University of Melbourne’s Melbourne Bioinformatics, utilising the Australian Research Data Commons (ARDC)’s Nectar Research Cloud and Pawsey Supercomputing Centre computational resources.

Galaxy Australia is an active member of the global Galaxy Project community and is supported by Bioplatforms Australia (through the Australian BioCommons initiative), ARDC, the University of Melbourne and the Queensland Government’s Research Infrastructure Co-investment Fund.

CloudStor is a cloud research data storage platform developed by AARNet for the Australian research and academic community. It is hosted on the AARNet network and offers integrated applications to support research workflows and allows users to store, share, describe and analyse data safely in one place. Users can access their CloudStor workspace from multiple devices, import data from a variety of sources and easily collaborate on files with colleagues at different institutions. Currently, users from every Australian University and CSIRO have access to a CloudStor allocation.

Dr Frankie Stevens, AARNet’s Deputy Director, eResearch, said an increasing number of life sciences researchers are using both Galaxy Australia and CloudStor for their work.

“The ability to streamline the secure transfer of data between the two platforms was a logical next step. This is a great example of how AARNet is collaborating with the research community to develop tools and services that meet the unique needs of researchers,” she said.

AARNet worked closely with the Galaxy team on the development of the integration under the leadership of Dr Gareth Price, Head of Computational Biology at QFAB and Service Manager at Galaxy Australia.

“Galaxy Australia users have a number of mechanisms to bring data easily into the platform, from their local computer, from websites and from international repositories. However, an important missing route into the platform was the secure transfer of data from CloudStor,” he said.

Now, with the release of the “Import from Cloudstor” tool users of Galaxy Australia can apply a simple configuration to their CloudStor storage allocation. This enables them to navigate to their folders and files and import directly into Galaxy. Additionally, a “Send data to CloudStor” tool allows, within the same web interface, a simple select and click secure transmission of data from Galaxy Australia into CloudStor.

TRAINING WORKSHOPS

Australian BioCommons and AARNet are collaborating to offer new training events for researchers who need to find solutions for their data movement challenges.

An interactive webinar, Back to basics: handling research data, will help bioscientists who are struggling to come to grips with research data movement.

The Practical tools for managing, moving and analysing data workshop will introduce CloudStor and its integration with data analysis solutions including Juypter Notebooks and Galaxy.

Registration is free but places are limited.

Register now

MORE INFORMATION

Learn more about Galaxy Australia

Learn more about AARNet CloudStor

Hear about our latest developments at eResearch Australasia

Many of the Australian BioCommons team and partners working on our projects will be presenting at the next eResearch conference. Here’s a grab of ways to hear about our ongoing developments:

Tue 20 October

12:00 The Australian BioCommons Bring-Your-Own-Data Platform: Integrating instruments, analysis tools and compute platforms for leadership bioinformatics

12:20 ARCOS: Findings from a roadmap to establish a national capability for containers

12:20 Galaxy Australia’s role in responding to the COVID-19 pandemic

13:30 BoF: COVID-19 eResearch Experiences and Collaborations in Australasia and Southeast Asia – Upskilling Support for Pandemic Response, Preparedness and Recovery

Wed 21 October

13:30 BoF: Nailed it: Moving digital skills training online

Thu 22 October

12:00 Galaxy Australia – a 2020 update

Fri 23 October

12.40 The recently signed Australian BioCommons / ELIXIR Collaboration Strategy Agreement allows for unprecedented cooperation on bioinformatics infrastructure between Australia and the EU

12.40 Addressing authentication and authorisation needs of the life science research community

14:40 Galaxy Australia and CloudStor (AARNet) – creating linkages between two national resources

Posters

An online bioinformatics training method delivering practical and tailored workshops to distant trainees

The Australian BioCommons Community Engagement Strategy: Engaging Researchers at a National Scale to Understand Challenges and Deliver Solutions

Pawsey boosts Galaxy Australia’s capabilities with COVID-19 grant

Australian researchers can now rapidly analyse their SARS-CoV-2 data using published tools and workflows by using a new dedicated Galaxy COVID-19 compute node hosted at Pawsey Supercomputing Centre. The ability of Galaxy Australia and Pawsey to jointly deliver this enabling data analytics platform has been made possible as part of the COVID-19 Accelerated Access Initiative in which Australia’s national HPC facilities responded quickly to the pandemic with streamlined, prioritised and expedited access to computation and data resources. NCI Australia and the Pawsey Supercomputing Centre have now announced that the Galaxy COVID-19 compute node would be hosted on Pawsey’s newly deployed Nimbus Cloud, guaranteeing tailored resources for urgent public health research. 

The new resource will deliver the benefits that were highlighted in the recent joint publication written by the international Galaxy team from Australia, Germany, Belgium and the USA who demonstrated how the Galaxy platform can facilitate the exchange of data and reproducible workflows between authorities, institutes and laboratories, ensuring that progress is no longer limited by access to samples and data. The compute allocation at Pawsey has been set up to exclusively underpin the use of the COVID-19 related tools and workflows outlined in that publication, on Galaxy Australia.

A national call out for Australian researchers tackling the COVID-19 pandemic resulted in seven projects receiving access to computation and expertise. Read the Leaders in Australian Computing Research Begin Battle with COVID-19 media release here.

Rapid, collaborative and transparent analysis of novel coronavirus on Galaxy Australia

Published in partnership with ARDC

Researchers from universities in Germany, Belgium, Australia and the USA, have used publicly available novel coronavirus (COVID-19) genome data and published their analyses using Galaxy, an open source research platform.

The joint paper, written by the international Galaxy team, demonstrates how the COVID-19 genome data can be shared, analysed and reproduced in an efficient and transparent way. In the wake of the COVID-19 pandemic, the researchers showed how Galaxy could facilitate the exchange of data and reproducible workflows between authorities, institutes and laboratories dealing with the virus. The international Galaxy platform, through the provision of highly accessible, globally shared data and analytics platforms, has the potential to transform the way biomedical research is performed. By offering access to data and an open and reproducible analytics environment, the Galaxy platform ensures that progress is no longer limited by access to samples and data.

The Australian Research Data Commons (ARDC) and Bioplatforms Australia have partnered with Australian BioCommons to ensure that Galaxy Australia maintains tools, workflows and reference datasets for the Australian research community. The ARDC investments have seen the Genomics Virtual Laboratory and Galaxy Australia become essential services for training and analysis in data-intensive biomedical research. The total investment in grants and compute allocations to all Genomics Virtual Laboratory and Galaxy related projects since 2012 was approximately $6.43M, of which $5.18M was in project grants and an estimated $1.25M in underpinning compute and data storage resourcing. This support was augmented by national coinvestment of $6.69M ($4.23M project co-investment plus (estimated) $2.46M compute provisioning) from the University of Melbourne, Queensland Cyber Infrastructure Foundation, Research Computing Centre (UQ), Bioplatforms Australia.

Through coinvestment from the ARDC’s Platforms Programs over the next three years, work is underway to broaden Galaxy Australia’s capabilities by increasing the communities that can use the platform and the types of analyses the platform can perform. The most recent "BioCommons BYOD [Bring Your Own Data] Expansion Project" Platforms grant of $2.21M will bolster the contributions of Australian BioCommons, University of Melbourne, Bioplatforms Australia, Australia’s Academic and Research Network, Australian Access Federation, National Computational Infrastructure, Pawsey Supercomputing Center, Queensland Cyber Infrastructure Foundation, Melbourne Bioinformatics, and Sydney Informatics Hub.

Associate Professor Andrew Lonie, Director of Australian BioCommons, says digital technologies are proving transformational for researchers in the life sciences domain:

“The enhanced Galaxy Australia platform will position Australia at the forefront of bioinformatics infrastructure and substantially improve Australian researcher’s access to bioinformatics.”

ARDC’s Director of Platforms and Engagement, Dr Andrew Treloar says the breadth of ARDC investment in research platforms ensures Australia's world class research system continues to improve productivity, create jobs, lift economic growth and support a healthy environment:

“It’s fantastic to be investing in research-orientated platforms and services that integrate and provide access to a range of resources to researchers and industry. This is a great opportunity to collaborate with our partners and universities at the cutting-edge of research to provide Australian researchers with competitive advantage through data.”

During an outbreak like the COVID-19, the development and implementation of effective infection control and prevention measures relies on the global research community’s ability to share data in a timely manner and perform fast and reproducible analyses. Platforms like Galaxy Australia can enable and accelerate this process. Read more about Galaxy Australia’s role in the recent COVID-19 study below and visit the ARDC website to find out how the ARDC is supporting an expansion of the Galaxy Australia project.

Galaxy Australia contributes to global research effort into COVID-19

The recent public health emergency arising from the COVID-19 outbreak has demonstrated the necessity for a rapid, collaborative and international response. The development of fast and effective countermeasures relies on the global research community’s ability to share data and perform fast and reproducible analyses. 

A joint paper by Galaxy teams from Australia, Europe and the United States demonstrated how the COVID-19 genome data can be shared, analysed and reproduced in an efficient and transparent way. The study “No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics” re-analysed all COVID-19 genomic data available in the public domain using Galaxy platforms and open software tools. The publication highlighted the inadequate accessibility of raw data associated with COVID-19 research, and described how the work completed on Galaxy opened up the possibility for any researcher worldwide to perform their own analyses with the data, analysis pipelines and public computational infrastructure freely available. 

The international Galaxy network provides highly accessible, globally shared data and analysis platforms, and offers the potential to transform the way biomedical research is done. By offering access to data and an open and reproducible analytics environment, it can ensure that progress is no longer hampered by access to samples and data. The various Galaxy facilities provide community-based infrastructure for research in recognition of exactly what the paper’s authors found: “there is a global need to ensure access to free, open, and robust analytical approaches that can be used by anyone in the world to analyze, interpret, and share data.”

This recent work involved Galaxy Europe (operated by ELIXIR Germany), usegalaxy.be (operated by ELIXIR Belgium and the Flemish Supercomputer Center), Galaxy US and Galaxy Australia. The Galaxy Australia team rapidly implemented the COVID-19 analysis workflows across Galaxy Australia’s distributed national compute infrastructure, operated by Melbourne Bioinformatics and the Queensland Cyber Infrastructure Facility. Galaxy Australia is widely accessible through its deployment on the Australian Research Data Commons’ (ARDC) Nectar Research Cloud and receives funding from the Australian BioCommons. 

All analyses performed by Galaxy teams are fully documented and accessible at:

https://github.com/galaxyproject/SARS-CoV-2/; https://doi.org/10.5281/zenodo.3685264

Accessible on Galaxy Australia at: https://usegalaxy.org.au/workflows/list_published; Tag: covid-19

Full paper available here: No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics Galaxy and HyPhy developments teams, Anton Nekrutenko, Sergei L Kosakovsky Pond, bioRxiv 2020.02.21.959973 doi: https://doi.org/10.1101/2020.02.21.959973

See also:

UseGalaxy, SARS-CoV-2 / COVID-19, and how effective responses to emerging pathogen threats require open data and open analytics: Galaxy Project

Coronavirus data analysis: Galaxy Europe

Open collaborative infrastructure to tackle public health emergencies: ELIXIR Europe

Galaxy Australia is hosted by the University of Melbourne and the Queensland Cyber Infrastructure Foundation and is enabled by NCRIS via Australian BioCommons funding through Bioplatforms Australia and the ARDC.

New investment to tackle the data challenges of bioscience researchers

A new investment from the Australian Research Data Commons (ARDC) will enable significant expansion of the Australian BioCommons ‘Bring Your Own Data (BYOD)’ Platform.

Earlier this year, discipline-focussed research-orientated platforms were invited to apply for investment to support better connections between data-related resources, industry and researchers. The Australian BioCommons submitted an application involving eight partner organisations: Bioplatforms Australia, Australian Access Federation, AARNet, National Computational Infrastructure, University of Sydney, University of Melbourne, QCIF and Pawsey Supercomputing Centre. The proposal, BioCommons Bring Your Own Data (BYOD) Expansion Project, detailed how this group would work together to build on the foundational work already being coordinated through the BioCommons.

We are delighted that the Australian BioCommons proposal has been successful in securing investment through the ARDC Platforms program.

The investment will enable the integration of data-generating instruments across genomics, proteomics and metabolomics, enhance accessibility to high-priority reference data, and manage access to compute infrastructures. It will support a wide range of Australian life science researchers by:

• Improving and expanding the established highly accessible Graphical User Interface (GUI)-based BYOD platform (Galaxy Australia), that gives all life sciences researchers, including informaticians, access to a well-structured, worlds-best-practice bioinformatics workbench for research and training.

• Developing a complementary Command Line Interface (CLI)-focussed BYOD platform, which will provide a scalable and flexible set of open programmatic resources to create, access and exchange workflows, tools and training across any national and institutional compute infrastructures.

• Developing a pan-national data infrastructure that will connect -omics instruments and reference datasets to the analysis infrastructure, underpinned by a capability to transport data nationally and internationally.

More information on the ARDC Platforms program is available on the ARDC website.