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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.
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.
MORE INFORMATION
Learn more about Galaxy Australia
Learn more about AARNet CloudStor
Conservation genomics collaboration helps research community
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.
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
12:20 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
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 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
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.
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 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
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.
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.
Australian BioCommons to address the bioinformatics challenges of Australian bioscientists
Australian BioCommons to address the bioinformatics challenges of Australian bioscientists
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 under the current contract.
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. 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).
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 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
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.
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.
Related stories:
https://www.genomeweb.com/cancer/seven-bridges-joins-international-genomic-cancer-research-effort
NEWS RELEASE: Seven Bridges Announces International Collaboration Focused on Personalized Treatment for Kids with Cancer
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.
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.
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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.