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Christina Hall 25/11/20 Christina Hall 25/11/20

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

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.

Christina Hall 26/10/20 Christina Hall 26/10/20

CloudStor integration for Galaxy Australia is now live

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.

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.

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

Rahul Ratwatte 26/10/20 Rahul Ratwatte 26/10/20

Conservation genomics collaboration helps research community

26 October 2020

This is the latest piece from the NCI’s Research Collaborations series - visit their website for the full story.

NCI’s strategic collaboration between and across conservation genomics research groups has enabled improved access to supercomputing, and enhanced development efforts to improve software and data resources. As an example, the Oz Mammals Genomics (OMG) Framework Data Initiative, supported by Bioplatforms Australia, has partnered with the Australian BioCommons and NCI to make bioinformatics tools more available for the genomics research community. OMG brings together dozens of researchers from across Australia and the world with interests in conservation around threatened and extinct species of Australian mammals.

The OMG projects generate genomic data sets to help understand population lineages, evolution, dispersal patterns, and the impacts of conservation management actions. With a focus on creating complete, high-quality genomes from animals such as the Fat-Tailed Dunnart and Marsupial mole, as well as population-level data sets for threatened species, samples are obtained from living animals collected in the field, and from specimens (including from extinct species) preserved in museum collections and research laboratories. Processing and analysing genomic data from mammals requires supercomputers and specially optimised software that takes advantage of the many parallel processors available. As a partner infrastructure in the Australian BioCommons, NCI has been helping to upgrade the capabilities of some key software tools, including the Canu de novo genome assembler.

Computational resources required for conservation genomics research are dispersed around the country, and there is a need to increase the expertise available to operate these systems. The national biological research organisation Bioplatforms Australia funded the OMG initiative in 2016 as part of a range of initiatives to improve the delivery of tools and methods for life sciences research. The OMG initiative and other Bioplatforms Australia Framework Initiatives, including Genomes of Australian Plants and the Threatened Species Initiative, are all helping to build a community-wide strategic approach to conservation genomics.

Dr Anna MacDonald, the manager of the OMG consortium of over 30 museums, universities, government agencies and non-government organisations, says, “Getting the momentum of the community behind this collaborative effort is a huge improvement. In a few years we’ve gone from very little coordinated use of computational methods to a really active uptake and constant improvements.”

Some of the research outcomes include supporting the on-going assembly of a high-quality genomic sequence at NCI for the marsupial mole, a rare burrowing marsupial found in the central deserts of Australia, and using population genomic data to evaluate translocations and guide conservation management of the burrowing bettong and rufous hare-wallaby.

Promisingly, the major benefits of OMG and the associated projects are still to come, says Australian BioCommons bioinformatics engagement officer Dr Johan Gustafsson.

“I’m very excited to see what comes next from this research community. We’ve built an important foundation and brought everyone to the table. The software improvements taking advantage of the Gadi supercomputer’s many parallel nodes will make a big difference in coming years.”

The conservation of endangered animal species through the genomics research undertaken in the multi-year OMG project has been fortified by the partnership with Australian BioCommons and NCI to improve the data, skills and tools available to researchers, and leverage expertise and computational resources. NCI compute resources and code optimisation expertise are playing a key role in the development of improved tools and techniques for genomics computation.

You can find out more about the Oz Mammals Genomics initiative at their website and in this paper.

Christina Hall 15/10/20 Christina Hall 15/10/20

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…

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

Christina Hall 31/8/20 Christina Hall 31/8/20

Associate Directors of the Australian BioCommons

Meet our Associate Directors and learn what excites them about our work.

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.

Christina Hall 31/8/20 Christina Hall 31/8/20

Rapid genome assembly on Gadi at NCI

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

Christina Hall 1/7/20 Christina Hall 1/7/20

Bioplatforms Australia charges Australian BioCommons with addressing our national bioinformatics challenges

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.

Rahul Ratwatte 9/6/20 Rahul Ratwatte 9/6/20

Australian BioCommons to address the bioinformatics challenges of Australian bioscientists

Australian BioCommons to address the bioinformatics challenges of Australian bioscientists

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. After engaging intensively with ELIXIR since 2017, a new alliance has evolved.

New strategic collaboration with ELIXIR

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.

Further information regarding the Collaboration Strategy is available here (password: ELIXIR).

Christina Hall 8/6/20 Christina Hall 8/6/20

New strategic collaboration with ELIXIR

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.

Christina Hall 5/6/20 Christina Hall 5/6/20

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

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