Chan Zuckerberg Initiative injects funds into Galaxy platform for biomedical research

28 January 2021

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.

New investment to improve human genomics data sharing for research in Australia

25 November 2020

A new investment from the Australian Research Data Commons (ARDC), Australian BioCommons and multiple partner organisations will transform how human genomics data for research is shared by bringing the best global technologies and standards to Australia. Through this new project, genomic data from thousands of Australians will be able to be shared securely and responsibly on national and global scales, enabling comparison with very large numbers of other genomes to ensure their full research value can be realised.

Working with key partners Zero Childhood Cancer, Australian Genomics Health Alliance, University of Melbourne Centre for Cancer Research, Garvan Institute of Medical Research, QIMR Berghofer Medical Research Institute, Australian Access Federation (AAF), National Computational Infrastructure (NCI) and Melbourne Bioinformatics, this 2.5 year project will implement standards and APIs developed by the Global Alliance for Genomics and Health, and also bring human genomic data holdings from participating efforts into alignment with the global human genome repository (European Genome-Phenome Archive (EGA)).

The project forms part of the Australian BioCommons Human Genome Informatics Initiative, and will deliver a services toolbox for improving FAIRness of genomic data at the institutions that hold most human genomes collected for research in Australia. The toolbox will include: systems to identify virtual cohorts nationally (i.e. across multiple human genomics repositories); tools to semi-automate data access request approvals; high assurance user authentication and user authorisation systems appropriate for human genome data sharing; and streamlined methods for metadata and data upload from Australia to EGA. Development of documentation and training materials and events to ensure researchers can use any systems implemented, and that other Australian providers/institutions can deploy similar resources will also be a key part of the project.

The funding component from ARDC resulted from a call for proposals for research-orientated platforms that enable researchers to collect or generate data, analyse that data and produce outputs that could be made Findable, Accessible, Interoperable, and Reusable (FAIR) and an investment to support transformative platforms that encouraged radical changes in the way research is conducted and/or dramatically increased the speed of research. For more information visit the ARDC announcement here.

CloudStor integration for Galaxy Australia is now live

26 October 2020

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

15 October 2020

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

Rapid genome assembly on Gadi at NCI

31 August 2020

The Australian BioCommons is identifying community-supported bioinformatics tools used for assembly of non-model organism reference genomes, and subsequently coordinating the install, optimisation and documentation of these tools across Australian computing facilities, including the national (tier 1) high performance computing centres. A major aim is to provide reusable and reproducible methods that can be applied across these and other infrastructures available to the genome assembly community.

The first tool considered by this activity was Canu, a long read assembly package for Nanopore and PacBio sequencing data. Collaboration between researchers from the Genomics for Australian Plants (GAP) consortium and specialists at the National Computational Infrastructure (NCI) resulted in a decrease in assembly time for the Golden Wattle (Acacia pycnantha Benth.) from more than 2 weeks on institutional resources to 3 days on the Gadi supercomputer. This was achieved using a wrapper script that makes distributed jobs from Canu compatible with the scheduler on Gadi: allowing the tool to make use of multiple nodes. The Gadi-optimised implementation of Canu is described in detail on the BioCommons GitHub Canu repository.

The success of this work has led to multiple additional activities:

Completion of the Waratah (Telopea speciosissima) genome assembly for GAP during a user test of the optimised Canu installation
Sharing of the optimised Canu with BioCommons stakeholder researchers
Additional optimisation and troubleshooting on Gadi for larger mammalian genomes (> 3 Gb) to support Oz Mammals Genomics (OMG)
Benchmarking activities for Canu to support merit applications by the bioinformatics community.

Australian BioCommons regularly engages with Australian bioscience research communities to document challenges and define requirements for shared bioinformatics resources. Please join the discussion with the Genome Assembly community to develop a vision for shared national infrastructure that will support your research. For further information: contact@biocommons.org.au

Associate Directors of the Australian BioCommons

31 August 2020

Dr Rhys Francis, Strategy and Partnerships

The Australian BioCommons is all about people using digital data as an ingredient in creating new knowledge. Delivering on that perspective involves the strategic use of e-infrastructures and capabilities and the promotion of new e-capabilities. Rhys brings a wealth of experience in those topics including authoring the NCRIS eResearch plan and working within government and the sector to propose and initiate much of Australia’s eResearch landscape all of which continues today. His interests over that time have steadily turned towards data as an ingredient in knowledge generation. He aims to make Australian BioCommons a flagship example of harnessing digital infrastructure for data driven knowledge creation.

Dr Jeff Christiansen, Engagements and Operations
How can the BioCommons deploy useful informatics solutions for many thousands of life scientists across the country that are fit for purpose and address a need? We believe through an inclusive culture of community engagement - where researchers are asked in the first place what their current challenges are, and where we listen carefully and distil this information down to identify useful approaches or solutions that can be deployed to address these community-scale challenges. We're also very keen that the community is fully included through all the stages of the journey.

Jeff leads the Engagement Team and brings an expert biological knowledge from a molecular biology research background and over 20 years of hands-on experience distilling researcher's challenges and then building fit for purpose and easy to use data-centric solutions for various communities of life science researchers. Digital technologies are proving transformational for the life sciences across the globe, and it's Jeff's aim to make sure that Australian researchers can participate fully in this global digital ecosystem as first class citizens through making sure the BioCommons coordinates deployment of things the community needs. It's a mammoth task, but if we can build solutions to address different communities needs and make sure these all work together seamlessly across Australia and internationally, we'll go a long way to achieving this goal.

Dr Steven Manos, Cyberinfrastructure

The mission to deliver transformational digital capabilities to Australian life scientists can only be realised though successful partnership with national digital infrastructure capabilities including NCI, Pawsey, ARDC, AARNet, AAF and others. An ambitious strategy using a cyberinfrastructure approach will drive the implementation through close collaborations with national and international stakeholders.

Steven brings 15 years of experience working at the intersection of research practice and digital technologies. He brings a mix of skills in facilitation, strategy and tech, and has a big focus on partnerships and community building. His work will deliver a more united national workforce of research support specialists providing valuable expertise and new services to the life sciences community.

Dr Nigel Ward, Platforms

BioCommons plans to deliver an ecosystem of platforms that provide researchers with sophisticated analysis and digital asset stewardship capabilities. The shape of these platforms will be defined through working closely with partner organisations during their establishment, operation, and interoperation.

Nigel brings many years of experience in applied IT research, software engineering, interoperability of distributed systems, web technologies, service and data standardisation to assist the teams establishing online software platforms, including overseeing the deployment of software platforms such as EcoCloud, Biodiversity and Climate Change Virtual Laboratory, Characterisation Virtual Laboratory, Humanities & Social Science Virtual Laboratory and Galaxy Australia.

BioCommons has a range of platforms with differing levels of maturity, from the well-established Galaxy Australia service running thousands of jobs per month, to the nascent command-line interface program that we are prototyping now. By engendering a "growth mindset" in the teams developing and operating these platforms Nigel will ensure that the BioCommons is responding systematically to new researcher needs identified through our community engagement process.

Sarah Nisbet, User Experience and Support
As the number of platforms and services steadily grow, harmonised user experience and support becomes increasingly important. With years of experience working across several organisations to roll out user support and service delivery systems, Sarah is passionate about delivering solutions for researchers. In her current role at Bioplatforms Australia Sarah is responsible for enhancing and extending cooperation and collaboration across various networks and capabilities. Sarah's new role will ensure that researchers have a streamlined and positive experience when using multiple Australian BioCommons platforms and services.

Bioplatforms Australia charges Australian BioCommons with addressing our national bioinformatics challenges

1 July 2020

The Australian BioCommons is proud to announce the signing of a contract with Bioplatforms Australia to deliver enhanced coordination in the planning and development of research infrastructure supporting bioinformatics in life science research. The $20M NCRIS investment will improve the ability of many of Australia’s best researchers to undertake leading edge bioinformatics analyses. The Australian BioCommons is partnering with a network of Australian and global bioinformatics and data intensive research groups to address high priority challenges through to 2023.

This significant milestone follows the success of the Bioinformatics Commons Pathfinder Project that actively engaged with the Australian bioscience community during 2019-2020. The Pathfinder activity established the Australian BioCommons as a sound investment avenue and a national bridge between the biosciences research community and both national and institutional digital resource providers. Working with national infrastructures including Bioplatforms Australia, the Australian Research Data Commons (ARDC), Australia’s Academic and Research Network (AARNet), Pawsey Supercomputing Centre, National Computational Infrastructure, Australian Access Federation, University of Sydney through Sydney Informatics Hub, Queensland CyberInfrastructure Foundation, Melbourne Bioinformatics and a raft of eminent universities and research institutes, it delivered exemplar bioinformatics services and generated cooperative research activities with new research communities. A powerful group of highly engaged partners now stand ready to provide guidance and implementation assistance to establish a national research infrastructure for biosciences, through the Australian BioCommons, that is closely aligned with international peers and supported through a combination of national and institutional funding.

The establishment of the Australian BioCommons follows several years of strategic discussions with national and international peers. The role of EMBL Australia Bioinformatics Resource, enabled by funding partners Bioplatforms Australia and the University of Melbourne, was pivotal in establishing an Australian national bioinformatics infrastructure network. This cooperative representation to the national government successfully leveraged national research infrastructure funding has been exceptionally well received by international peers, as demonstrated by our recent Collaboration Strategy with ELIXIR since 2017, announced here.

New strategic collaboration with ELIXIR

8 June 2020

A new Collaboration Strategy between ELIXIR and the Australian BioCommons seeks to create a cooperative plan to exploit international synergies between the two research infrastructures. This three-year collaboration will actively involve Australian BioCommons in many of the activities related to the European life science infrastructures.

A number of common alignment areas have been identified for future collaboration including the adoption of international standards in software platforms, workflows, tools and data (such as the Global Alliance for Genomics and Health (GA4GH)). Supporting global research communities (such as in metagenomics methods, biodiversity, de-novo genome assembly, phylogenomics, plant phenotyping-genotyping), and the delivery of federated solutions to human data preservation and research access are prime examples of why these partners have come together to formalise a Collaboration Strategy.

ELIXIR and the Australian BioCommons are both already heavily involved in methodological platform and tool collaboration — a leading example of a joint project of interest being Galaxy, the open, web-based platform for collaborative research. International collaboration on training and training materials in bioinformatics has also begun, with ELIXIR Training Platform partners participating in the Australian BioCommons Training Advisory Group. Such initiatives will continue to strengthen links between BioCommons and ELIXIR over the course of this agreement.

Following years of fruitful discussions about shared challenges, including during reciprocal study visits, there was a realisation that the work programmes of both organisations align strongly in many areas. Both Australian Biocommons and ELIXIR coordinate distributed resources for biological research and together represent broad international perspectives on research infrastructure for the biosciences. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. Resources including databases, software tools, training materials, cloud storage and supercomputers are coordinated so that they form a single infrastructure. Making it easier for scientists to find and share data, exchange expertise, and agree on best practices ultimately helps them gain new insights into how living organisms work.

The collaboration strategy between ELIXIR and the Australian BioCommons promises to identify our international synergies as we partner to tackle our shared challenges in biological research.

ELIXIR’s news release can be read here.

Further information regarding the Collaboration Strategy is available on our website here and on ELIXIR’s website here.

Australian BioCommons partners with international collaboration focused on personalised treatment for kids with cancer

5 June 2020

Industry-leading bioinformatics ecosystem provider, Seven Bridges, sparked international interest this week in the multinational genomic cancer research project that Australian BioCommons contributes to. Their media release Seven Bridges Announces International Collaboration Focused on Personalized Treatment for Kids with Cancer documented how our collaboration will help researchers better understand rare pediatric brain cancer subtypes and improve interventions for patients and their families. Working with Seven Bridges, The Gabriella Miller Kids First Data Resource Center (Kids First DRC), ZERO Childhood Cancer (ZERO), the Children’s Brain Tumor Tissue Consortium (CBTTC) and the Australian Research Data Commons (ARDC), we are establishing internationally federated computational infrastructure that will enable the harmonisation of pediatric cancer data from ZERO Australia with the extensive genomic datasets from CBTTC and Kids First DRC.

So far the team has been working hard on the complex challenge of harmonised analysis of geographically separated and jurisdictionally protected data resources. Cavatica, a cloud-based platform for collaboratively accessing, sharing, and analysing cancer data has been expanded to AWS Sydney. Key members of the team from the Center for Data Driven Discovery in Biomedicine (D3b) at the Children's Hospital of Philadelphia traveled to Australia earlier this year to boost our local ability to leverage Cavatica's benefits and the story was written up here.

The Australian Government, together with the Minderoo Foundation, recently announced an additional $67 million for personalised treatments for every child with cancer. The investment will directly support the ground breaking Zero Childhood Cancer Personalised Medicine Program (ZERO) that is working to ensure children and young people diagnosed with cancer are given the greatest chance of survival. Expanding the program from approximately 150 children per year to 1,000 children per year all Australian children and young adults diagnosed with cancer will now have access to genomically-guided, precision treatments through this world leading collaborative research and clinical program.

With the expansion of the ZERO Program in Australia and the compelling progress made by the international collaboration towards the seamless sharing of data and analysis methods between researchers in Australia and the United States, we look forward to sharing more exciting updates soon.

Seven Bridges media release

NEWS RELEASE

Seven Bridges Announces International Collaboration Focused on Personalized Treatment for Kids with Cancer

Expansion of the CAVATICA Platform to Australia Enables Harmonized Analysis of Geographically Separated and Jurisdictionally Protected Data Resources

BOSTON, June 2, 2020—Seven Bridges, the industry-leading bioinformatics ecosystem provider, today announced a collaborative partnership between The Gabriella Miller Kids First Data Resource Center (Kids First DRC), ZERO Childhood Cancer (ZERO), the Children’s Brain Tumor Tissue Consortium (CBTTC), the Australian BioCommons and the Australian Research Data Commons (ARDC). The multinational genomic cancer research project aims to establish internationally federated computational infrastructure that will enable the harmonization of pediatric cancer data from ZERO Australia with the extensive genomic datasets from CBTTC and Kids First DRC. Through this collaboration, researchers hope to better understand rare pediatric brain cancer subtypes and improve interventions for patients and their families.

Large-scale cancer whole genome sequencing (WGS), RNA-Seq and methylome analyses have made a substantial impact on our understanding of many cancers, including their etiology, identifying disease subtypes, novel pathways and new drug targets. While there are a number of extensive genomic cancer research programs globally, most focus on adult cancer; however, as all high-risk pediatric cancer subtypes are rare diseases, statistically significant correlation between subtype and genomic variation is inherently dependent on large sample numbers.

“Childhood cancer kills more children than any other disease in Australia and every week three children and adolescents in Australia die because of cancer,” said Mark Cowley, Ph.D., Associate Professor of the Children’s Cancer Institute. “Every child is different, every cancer is unique, so treatment has to be tailored for each individual. Through an international data collaboration on pediatric cancer subtypes, we hope to better understand how to treat the cancers we find in Australia, based on information that was previously unaccessible.”

Research will be done on the CAVATICA Platform, a cloud-based system for collaboratively accessing, sharing and analyzing childhood cancer data. The CAVATICA Platform, powered by Seven Bridges, allows clinicians and scientists worldwide to rapidly access large amounts of genomic data and workflows within a computation and storage environment where they can share, process, integrate and analyze data. Complex and comparative analyses can be achieved using various open source R and Python packages; and through the Data Cruncher feature, data can be shared through interactive Jupyter Notebooks.

“The CAVATICA Platform enables us to seamlessly collaborate, share, interoperate and connect with other researchers studying pediatric cancer, driving improved outcomes and novel research,” said Adam Resnick, Ph.D., Kids First Data Resource Principal Investigator. “The platform has enabled us to harmonize and process over 15,000 whole genomes, whole exomes and RNA-seq, including alignment, somatic variant calling, copy number calls, structural variants, RNA expression and fusions. Additionally, integrations with the Kids First Data Resource Center portal allow users to create cohorts and manage their analysis in secure, cloud-based projects in CAVATICA.”

To enable this multinational collaboration, the CAVATICA Platform is being expanded to enable harmonized analyses across geographically separated and jurisdictionally protected data datasets, in this case across Australia and the United States. The extended CAVATICA orchestration engine will allow ZERO and Kids First workflows and analysis tools to be used interchangeably and seamlessly across both datasets. From the researcher’s perspective, the platform aggregates the separate datasets into a single virtual pan-continental dataset that is highly accessible through a global best practice analysis platform.

“By connecting pediatric researchers across international borders through the CAVATICA platform, we are also breaking down borders between data silos through the use of the global standard Common Workflow Language (CWL) and the ease of multi-cloud computing,” said Brandi Davis-Dusenbery, Ph.D., Chief Scientific Officer of Seven Bridges. “This enables our researchers to focus on treatments for kids with rare cancers rather than data challenges.”

About Seven Bridges
Seven Bridges enables researchers to extract meaningful insights from genomic and phenotypic data in order to advance precision medicine. Our complete bioinformatics ecosystem consists of a compliant analytics platform, seamless data and automation, and expert scientific services. This holistic approach to bioinformatics is enabling researchers — at the world’s leading academic, biotechnology, government, medical centers, and pharmaceutical entities — to increase R&D efficiency, enhance the hypothesis resolution process, isolate critical biomarkers, and even turn a failing clinical trial around while also reducing computational workflow times and data storage costs. To learn more, visit sevenbridges.com or follow us on LinkedIn and Twitter.

About The Gabriella Miller Kids First Pediatric Research Program Data Resource CenterThe NIH Common Fund-supported Gabriella Miller Kids First Data Resource Center (Kids First DRC) is a collaborative pediatric research effort created to accelerate data-driven discoveries and the development of novel precision-based approaches for children diagnosed with cancer or a structural birth defect using large genomic datasets. The Kids First DRC is comprised of integrated core teams that support development of leading-edge big data infrastructure and provide the necessary resources and tools to empower researchers and clinicians.

As part of the Common Fund’s Gabriella Miller Kids First Pediatric Research Program, the Kids First DRC is charged with:

Developing data-driven platforms that integrate large amounts of genomic and clinical data from different disease types.
Empowering the collaborative discovery, engagement, and necessary partnerships across disease communities that are crucial for progress in our biological understanding of diseases.
Enabling rapid translation to personalized treatments for patients diagnosed with childhood cancer or structural birth defects.
Accelerating discovery of genetic causes and shared biologic pathways within and across these conditions.

About the Children’s Brain Tumor Tissue Consortium
The mission of the Children’s Brain Tumor Tissue Consortium (CBTTC) is to find cures and improve treatments for children diagnosed with brain tumors. To that end, the CBTTC collects high-quality brain tumor biospecimens and associated clinical data to facilitate the genomic analysis of biospecimens. Cell lines are developed and transplantable tumor models are then created from tumor specimens. These models allow researchers to share their findings with other CBTTC member institutions and with the world-wide scientific community. The CBTTC has established a collaborative multi-institutional tissue and data repository to enable the collection and analysis of high-quality brain tumor specimens. In addition to specimen data, the repository also links to clinical data to provide a comprehensive snapshot of each unique tumor.

Additionally, the CBTTC is committed to the advancement of tissue-based research, allowing researchers throughout the world to access molecular analysis of brain tumor specimens. These initiatives will allow for improvements in therapeutic treatment of patients diagnosed with a brain tumor.

About the Australian BioCommons
The Australian BioCommons is building digital capability for Australian life science research through the coordination and provision of bioinformatics and bioscience data infrastructures at a national scale. With a focus on active engagement with research communities, shared digital infrastructures are being developed and maintained in partnership with international peer infrastructures. The Australian BioCommons is tailoring services that provide sophisticated analysis capabilities, including both software and hardware platforms. Training and support solutions are streamlining access to the digital techniques, data and tools that are essential to environmental, agricultural and biomedical research. For more information online about the Australian BioCommons follow us on Twitter.

About Children’s Cancer Institute
Originally founded by two fathers of children with cancer in 1976, Children’s Cancer Institute is the only independent medical research institute in Australia wholly dedicated to research into the causes, prevention and cure of childhood cancer. Forty years on, our vision is to save the lives of all children with cancer and improve their long-term health, through research. The Institute has grown to now employ over 300 researchers, operational staff and students, and has established a national and international reputation for scientific excellence. Our focus is on translational research, and we have an integrated team of laboratory researchers and clinician scientists who work together in partnership to discover new treatments which can be progressed from the lab bench to the beds of children on wards in our hospitals as quickly as possible. These new treatments are specifically targeting childhood cancers, so we can develop safer and more effective drugs and drug combinations that will minimise side-effects and ultimately give children with cancer the best chance of a cure with the highest possible quality of life. More at www.ccia.org.au.

About Zero Childhood Cancer (ZERO)
The Zero program is led by Children’s Cancer Institute and the Kids Cancer Centre at Sydney Children’s Hospital, Randwick bringing together all major Australian clinical and research groups working in childhood cancer to offer Australia’s first ever personalised medicine program for children with high-risk or relapsed cancer.

About the Australian Research Data Commons
The Australian Research Data Commons (ARDC) is a transformational initiative that enables Australian research community and industry access to nationally significant, leading edge data intensive eInfrastructure, platforms, skills and collections of high-quality data. Our purpose is to provide Australian researchers competitive advantage through data. For more information visit online or follow us on LinkedIn and Twitter.

###

Media Contacts

Eric Schubert
Seismic for Seven Bridges
+1 415 692 6799
sevenbridges@teamseismic.com

This press release first appeared on the Seven Bridges website.

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

21 April 2020

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.

Progress on national plan for Containers and K8s

19 March 2020

Members of our team recently advanced the Australian BioCommons Software and Containers project by participating in two strategic meetings at Pawsey Supercomputing Centre in Perth. The March events drew together partners who are contributing to the national roll out of a common bioinformatics software containerisation and meta-data standard, and a common implementation standard of the open-source container-orchestration system Kubernetes for use by Australian life scientists.

Kubernetes (K8s) is an open-source system for automating deployment, scaling, and management of containerized applications. It groups containers that make up an application into logical units for easy management and discovery. Kubernetes is currently used by many individual research groups in Australia, but there is no currently no communication, coordination or local support for the service.

Two days of strategic discussions took place during the Australian BioCommons Software and Containers Workshop and the ARDC-funded National Kubernetes Core Services Planning Meeting. The workshop reviewed the ongoing progress of a large collaborative project led by the Australian BioCommons to identify the use cases for a coherent environment around containers and to coordinate the essential elements required to build the interoperable national infrastructure. The Planning Meeting discussed the implementation of a national eResearch program for supporting container orchestration and the use of Kubernetes.

A large group representing significant stakeholders including Pawsey, Australian BioCommons, ARDC, NCI, AARNet, ELIXIR Europe (remote attendance), CSIRO, Monash University, Melbourne University, Intersect, University of NSW, University of Tasmania/ TPAC, University of Queensland/ RCC, QCIF and University of Sydney worked together to define their next steps in the national Kubernetes plan.

These strategic meetings followed on from ten days of hands-on training by HPCNow! to upskill the Pawsey operations and end-user support teams in the Kubernetes system. Read more about Pawsey’s growing expertise in container orchestration solutions here.

We’ll keep you updated on how this coordinated effort will provide new bioinformatics solutions for Australian research community.

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

Tuesday 17 March 2020 (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

Thursday 27 February 2020

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

Seamless sharing of childhood cancer data and analysis between researchers across international borders

Friday 14 February 2020

The development of personalised treatments that target rare paediatric cancer subtypes can be enhanced through global collaboration. Comparing an Australian patient's tumour to a larger group of other tumours allows insights that lead to better outcomes. But geography and rules to protect personal data in different jurisdictions can make the sharing and comparing of essential data difficult or even impossible.

In an effort to fix this, the Australian BioCommons is part of an international collaboration that came together in Sydney this month. Members of the partnership between the Australian BioCommons, BioPlatforms Australia, ARDC, Children’s Cancer Institute, D3b and Seven Bridges have been working to provide an integrated bioinformatics research platform with compute, storage, and file metadata tagging all in one place.

“This multinational project is establishing internationally federated computational infrastructure to enable the harmonisation of pediatric cancer genomic data from Australia’s ZERO Childhood Cancer Program and the Gabriella Miller Kids First Data Resource Centre in the United States. ”

Australian initiatives such as Zero Childhood Cancer will leverage the benefits provided by Cavatica, through its expansion to AWS Sydney. Cavatica is a cloud-based platform for collaboratively accessing, sharing, and analysing cancer data.

Cavatica was launched in 2016 as a partnership between the Center for Data Driven Discovery in Biomedicine (D3b) at the Children’s Hospital of Philadelphia (CHOP), Seven Bridges, the Children’s Brain Tumor Tissue Consortium (CBTTC) and the Pacific Pediatric Neuro-Oncology Consortium (PNOC). Since then, it has expanded to being a collaborative platform for a number of initiatives, including the Gabriella Miller Kids First Data Resource Center (KFDRC).

AWS compute is leveraged allowing for high-throughput analysis, while workflows written in common workflow language (CWL) with docker to maximise portability and reusability. Additionally, via Cavatica’s Data Cruncher, analyses using various open-source R and Python packages can be shared through Jupyter Notebook. The KFDRC has used this platform to harmonise and process over 15,000 whole genomes, whole exomes, and RNA-seq, including alignment, somatic variant calling, copy number calls, structural variants, RNA expression and fusions.

During the visit, key members of the D3b team provided training in using Cavatica and Dr Allison Heath, Director of Data Technology and Innovation, Center for Data Driven Discovery in Biomedicine (D3b) at the Children's Hospital of Philadelphia kindly delivered an overview of Cavatica's features for the Australian BioCommons webinar series while she was in our time zone!

The intensive days together brought closer the reality of the platform’s readiness for use by Australian researchers in coming months. Stay tuned as Cavatica will soon be enabling seamless sharing of data and analysis methods between researchers in Australia and the United States.

New investment to tackle the data challenges of bioscience researchers

Thursday 19 December 2019

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.