Participating in the global ecosystem of responsible human genomics data analysis

Members of the BioCommons team have recently returned from the US where they progressed our mission to establish infrastructure for human genome sharing and analysis in Australia and to deliver the technical solutions needed to help researchers actively participate in global research collaborations. 

Uwe Winter, Marion Shadbolt, and Steven Manos met with key peers to bolster our understanding of world leading infrastructure to support human genome informatics which we are enhancing and deploying nationally. During their trip to the US between 9-17 May 2022, the group considered the essential elements of good national infrastructure, and brought home key learnings around the architecture, systems, user support, people and partnerships that are required. Our international partners reported that BioCommons’ ability to describe the Australian landscape and represent our researchers’ unique context and requirements was extremely valuable.

Starting in Chicago, our staff could finally meet in person with collaborators at the Center for Translational Data Science, University of Chicago. Sharing insights with Bob Grossman and his team, who are responsible for the Gen3 data platform, allowed deeper understanding of how Gen3 might support the interoperation and creation of cloud-based data resources, including data commons and analysis workspaces. Gen3 is already used internationally to manage, analyse, harmonise, and share large and complex datasets in the cloud and BioCommons activities are seen as a valuable opportunity to expand the Gen3 community.

Visiting the Center for Data Driven Discovery in Biomedicine at the Children’s Hospital of Philadelphia (CHOP) provided a boost to an important project that has been underway since 2020. Along with Seven Bridges and CHOP, Australian BioCommons is delivering impact to Australian researchers by participation in a global data commons, through the implementation of the cloud-based platform, CAVATICA, to facilitate collaborative access, sharing, and analysis of paediatric cancer data. Deeper collaboration was discussed with a view to further supporting Australia’s Zero Childhood Cancer Program.

The trip concluded in Boston where the team was hosted by the Broad Institute. The meeting offered a technical deep dive into the scalable platform for biomedical research, Terra, that enables researchers to access data, run analysis tools, and collaborate. Terra is used by over 25,000 (mainly US) researchers and valuable discussions were had about how it might integrate with Australian requirements.

These intensive fact-finding missions with international partners are an important element of Australian BioCommons mission to build the necessary foundations that ensure Australian researchers can participate fully in the global ecosystem of responsible human genomics data analysis. Our Human Genome Informatics Initiative continues to work towards infrastructure for global best practice human genome data warehousing, sharing and analysis in Australia.

Finding and reusing workflows made simple

Bioinformatics workflows bring together software packages into complex multi-step processes that standardise analysis.

Reuse of workflows can benefit life science researcher communities by accelerating their research, reducing replication of effort and supporting the application of best practice bioinformatics. Discoverability and reuse of workflows can also increase the visibility and recognition for bioinformaticians who invest large amounts of time, effort and intellectual property in workflow development.

The discovery and re-use of workflows is supported by the WorkflowHub registry that facilitates the description, sharing and publishing of scientific computational workflows, with applications ranging from eukaryotic and bacterial genome assembly to shotgun metagenomics.

After consultations with local researcher communities and participation in international forums discussing the shared challenge of workflow discoverability, the Australian BioCommons responded by establishing a presence on WorkflowHub. Converging on this resource together with our infrastructure partners and by working with the ELIXIR development team, the BioCommons team has worked to make the platform more fit-for-purpose for Australian bioscientists. The BioCommons and its partners have so far registered 31 workflows, which have already accumulated more than 16,000 views and 250 downloads.

The BioCommons has also established WorkflowFinder, which draws metadata from WorkflowHub and combines this with useful local information. In time this service will allow researchers to click and deploy workflows to local platform services. Right now it offers an interactive table that allows you to search for workflows registered by Australian BioCommons partners on WorkflowHub and details useful information such as where workflows have been successfully run in Australia.

Participating in a National Approach to Genomic Information Management

Australian Genomics recently released Preliminary Implementation Recommendations to the Australian Government (April 2022) to progress the development and establishment of a National Approach to Genomic Information Management (NAGIM) for Australia.

Australian BioCommons took part in the development of prototype components of the proposed NAGIM research ecosystem in 2021. Genomic data infrastructure stakeholders nationally were invited to participate in prototype development, in an open call leveraging existing capabilities/funding. BioCommons and others were tasked with addressing the identified priority areas, with the goal of identifying the best combination of components that can serve as the basis for long-term national research infrastructure.

An international expert panel was convened to advise and evaluate the NAGIM Blueprint Implementation prototypes and the collaborative submission made by Australian BioCommons’ Human Genomes Platform Project and the University of Melbourne Centre for Cancer Research was very favourably reviewed. BioCommons are listed as demonstrated NAGIM exemplars for several proposed workstreams and deliverables to support the NAGIM Implementation recommendations.

The latest report outlines the preliminary implementation recommendations for NAGIM, informed by the international panel’s NAGIM prototype evaluations, and parallel stakeholder consultation. Feedback is currently being sought on these recommendations from all stakeholders including research and clinical data communities, patient advocacy groups, Aboriginal and Torres Strait Islander genomic experts, industry, government representatives and agencies. Feedback will inform the development of a full report of the NAGIM Implementation Recommendations and proposed strategy for progressing NAGIM, which will be delivered to Government mid-year.

Stakeholders are encouraged to read the Preliminary Implementation Recommendations and to provide feedback by responding to the targeted questions in the online form by 5 pm AEST 17 June 2022.

At last: local team finally travels to join international Galaxy community

The Galaxy Australia team is thrilled to be jetting off to the Galaxy Community Conference in Minneapolis, USA from 17-23 July. GCC2022 will bring together hundreds of researchers, trainers, tool developers, software engineers, and computational infrastructure providers, all addressing common challenges in data intensive science using the Galaxy data integration and analysis platform.

The chance to meet up in person with the vibrant global Galaxy community has been sorely missed during the past couple of years, so members of the Galaxy Australia team jumped at the chance to discuss their work at the upcoming conference. Here’s a list of the speakers that will make presentations representing the excellent work of the much larger Galaxy Australia team:

• Nuwan Goonasekera and Catherine Bromhead, from Melbourne Bioinformatics at the University of Melbourne, will present their talk ‘Metascheduling Galaxy jobs with Total Perspective Vortex’

• Gareth Price, from QCIF at the University of Queensland, will offer a talk on ‘Galaxy Australia: an Evolving Scientific Instrument’

• Anna Syme, from Melbourne Bioinformatics at the University of Melbourne, will present ‘Creating Galaxy workflows to empower research into Australia's unique fauna’

• Cameron Hyde from QCIF at the University of the Sunshine Coast will present two posters: ‘AlphaFold on Galaxy - fast and accurate modeling of protein structure’ and ‘Galaxy Media Site - a full featured landing site for Galaxy Australia’.

Poster and demo abstracts will be accepted until 3 June 2022. GCC2022 features separate Training Day, Meeting, and CoFest events, which can be registered for separately or all at once, with significant discounts are offered to students and postdocs.

Program and registration information

Have your say on the new Biomedical Data Asset

The Biomedical Data Asset project aims to link two of Australia’s most important biomedical data sets in a highly curated environment for the community. It is a partnership between ARDC, Bioplatforms Australia, Phenomics Australia, Monash University and the Australian National University with engagement support provided by the Australian BioCommons. You have the chance to guide its development by filling out a quick survey.

The Biomedical Data Asset will combine human and animal model system data into one user-friendly and accessible environment. This will improve the functional understanding of genetic contributions to health and disease by synergistically boosting clinical management and biomedical research. Access to the biomedical data made available through this project will improve researcher ability to discover and experimentally validate gene function to improve diagnosis and treatment, especially in clinical human studies where genomic technologies have been used to identify genetic variation in relation to disease. 

These data collections are:

• The Aspirin in Reducing Events in the Elderly (ASPREE) study enabled through Monash University. ASPREE is a genomic and clinical data set from thousands of healthy older Australians.

• The mouse Missense Mutation Library (MML) created and curated at the Australian National University and enabled by Phenomics Australia. MML is a genomic and phenotypic database and biorepository of known variant missense and nonsense variant mice.

The Biomedical Data Asset project seeks the input of Australian researchers who are using, or planning to use, cross-species genomic and phenomic data sets in the medical or health sciences. Help create the Biomedical Data Asset by sharing your needs via the survey before 13 June.

Complete the 10-minute survey

New RDA Life Science Data Infrastructures Interest Group

RDA's 19th Plenary will be held 20-23 June as part of International Data Week 2022, with attendees welcome both in Seoul, South Korea and on online.

The Plenary will launch the new RDA Life Science Data Infrastructures Interest Group which Australian BioCommons is thrilled to chair with colleagues from the USA (Data Science at NIH and the Joint Genome Institute), Europe (ELIXIR) and Africa (H3ABioNet). The Interest Group will focus on data and computational infrastructures to support life science globally, comparing our contrasting our experiences and discussing topics of common interest.

The new Interest Group welcomes all who wish to contribute to this global conversation, so please join online on Wednesday 22 June at 09:30-11:00 AEST for the first meeting.

Better access to compute, expertise and tools accelerates valuable data generation

The Australian BioCommons is enabling rapid insights into life science community data assets using high end computing through its Australian BioCommons Leadership Share, also known as ABLeS. ABLeS is allowing life science research consortia to jointly access and collaboratively use Australia’s national computing facilities - the National Computational Infrastructure (NCI) and Pawsey Supercomputing Research Centre - offering computational resources, specialist expertise, centrally supported tools and software through and a shared repository of tools and software, tailored to support the generation of valuable reference data assets.

The benefits of generating  life science reference datasets - such as reference genomes or continental-scale of environmental microbiome analyses - are far-reaching, where research for health, agriculture and the environment all benefit. Bioplatforms Australia and many of its co-funding partners enable the generation of these reference datasets to address themes of national significance through Bioplatforms Australia’s Framework Initiative projects.

To date, these large collaborative efforts have been impeded by challenges around access to appropriate high-powered computational and storage infrastructure. The lack of access, available scale and technical support have limited the ability of research communities to converge on the construction of shared reference datasets from raw data, which also limits the ability to analyse these datasets to generate new scientific insights and knowledge. 

The core purpose of  ABLeS - the Australian BioCommons Leadership Share is to directly address these challenges and accelerate the generation of reference datasets, by facilitating researchers’ use of computational resources at Australia’s national computing facilities, the National Computational Infrastructure (NCI) and the Pawsey Supercomputing Research Centre.

The intention of ABLeS is to grow and accelerate our national ability to construct, maintain and gain insights from community defined and developed data assets (e.g. reference genome assemblies). ABLeS aims to provide communities with access to the necessary infrastructure to create those assets. At this stage, ABLeS is working with selected Framework Initiatives prioritised by Bioplatforms Australia, including Threatened Species Initiative, Genomics for Australian Plants, Australian Amphibian and Reptile Genomics, Plant Pathogen Omics Initiative andAustralian Grasslands and Adaptation Framework, as well as national science consortia such as Zero Childhood Cancer. Other communities and resources will be incorporated as the program matures.

A paper acknowledging ABLeS support has already been published, recognising that the authors accessed the scheme for their assembly of the genome of the Australian lizard, Tiliqua rugosa. University and museum researchers from Australia, New Zealand and the US, combined their ABLeS resources with multiple international grants to publish Comparison of Reptilian Genomes Reveals Deletions Associated with the Natural Loss of γδ T Cells in Squamates in the Journal of Immunology. With many more research communities receiving ABLeS support to generate valuable data assets, important publications across a diverse range of domains will follow.

Find a detailed description of ABLeS in the publication Building community data assets for life sciences through ABLeS - the Australian BioCommons Leadership Share.

For details of the resources, processes, eligible communities and contacts visit the ABLeS website.

A new streamlined Galaxy Australia interface

You may have already noticed a new streamlined interface when submitting your latest job to Galaxy Australia. If not, it’s time to check out the refreshed Galaxy Australia landing page!

Important functions in Galaxy Australia have been streamlined, including access to the tutorial library and support requests for tools and data. The comprehensive improvements to the user interface mean the landing page has updated news and events tables, and more accurate acknowledgement of Galaxy’s partnerships. 

“These updates are a part of an ongoing phase to improve the user experience of Galaxy Australia. We have brought together a group of Galaxy experts, designers and developers to continue to push the envelope of what is possible with the service and ensure that it continues to provide the latest in life science analytics in the most user friendly manner - the key to Galaxy success as such an accessible and useful service.” Madeline Bassetti, Galaxy Australia’s UI/UX Designer

Galaxy Australia welcomes feedback as they move through this development, so if you’d like to share your thoughts on the new design, please contact help@genome.edu.au.  

Galaxy functionality is also undergoing constant development by the international team, with updates announced regularly. The latest release of Galaxy 22.01 offered a wide range of improvements.

• New Colour Selector: Do you use tools which require colour inputs, like Circos? You now have complete freedom of choice for your colour palette.

• Improved File Uploads: A new upload method makes file uploads significantly smoother, and will be more tolerant of network failures and interruptions. 

• Improved File Export: The amazing new remote file source export allows you to export files from Galaxy to FTP, Dropbox, and other locations.

• Beta History: Collection Improvements: The beta history (which will be the default history in the next release in mid 2022) has been updated to indicate whether collections are homogeneous or heterogeneous. This will save you time and difficulties if you mistakenly build a collection containing variability likely to cause your downstream analysis to fail.

• Galaxy starts as a FastAPI application by default: Galaxy now supports interruption free restarts, allowing the Administrators to keep the service running whilst you keep analysing.

• User Preferences can be encrypted in Galaxy Vault: Galaxy can now be configured to store secrets in an external vault, which is useful for secure handling and centralisation of secrets management. 

Check out the Galaxy 22.01 announcement for an overview and short videos explaining the improvements, or read the full release notes for (a lot more) details and instructions for upgrading your Galaxy installation.

ToolFinder - discover and reuse bioinformatics software

Australian researchers have access to thousands of bioinformatics software packages. These are essential parts of their analysis pipelines, and having access to the right software is key to keeping research moving. The challenge is that this software is also widely distributed across a diverse system of national and institutional computing facilities and cloud platforms in Australia. When searching for the software packages they need, life scientists face a complex ecosystem that can be a complicated and confusing impediment to their work. 

In community consultations the Australian BioCommons heard the need to enhance the discoverability of bioinformatics software: our response is ToolFinder.

ToolFinder is a searchable and interactive table of software versions installed across Australian computational infrastructures. Information about what software is available at different locations is paired with useful metadata from the international software registry bio.tools. ToolFinder can therefore also provide information such as software homepage links, registered publications, available containers, licenses and more. 

The compute systems currently incorporated in ToolFinder include the Gadi high performance computer at the National Computational Infrastructure (NCI), the Zeus and Magnus machines at Pawsey Supercomputing Research Centre, the shared software system for QRISCloud and the cloud service, Galaxy Australia. It can be extended to include virtually any computational system in the country, and more systems are being listed over time.

ToolFinder was designed to aid navigation of the complex and distributed Australian bioinformatics ecosystem. It continues to be actively developed to ensure that it is practical and easy-to-use for Australian life science researchers. 

Check out ToolFinder now by searching or browsing by software name or purpose.

Providing researchers access to essential genome annotation tools

Community consultations are an opportunity for researchers to describe their challenges and research infrastructure needs. BioCommons has worked with a growing number of researcher communities who self-nominate around particular informatics methods. In response to requests from the Genome Annotation community for automatic genome annotation pipelines, BioCommons has made Fgenesh++ available for use by Australian-based research groups and research consortia.

Fgenesh++ is a bioinformatics pipeline for automatic prediction of genes in eukaryotic genomes. It can produce fully automated genome annotations of a quality similar to manual annotation, and is extremely fast compared to some other automated genome annotation pipelines.

It works by: (a) performing ab initio gene prediction; (b) running predicted amino acid sequences of all potential exons through a non redundant protein sequence database; and (c) running a second round of gene prediction with higher scores assigned to exons homologous to known proteins. 

To overcome the hurdles that many researchers face when wanting to try out licensed software, BioCommons entered into an agreement with Softberry that allows for a limited number of users to share access to Fgenesh++. Access is through a booking system which is managed by the Pawsey Supercomputing Research Centre.

BioCommons’ Community Engagement Officer, Dr Tiff Nelson, oversaw the provisioning of Fgenesh++ and has been impressed to see its rapid uptake:

It is great to have already facilitated the annotation of novel animal and plant genomes for the benefit of both conservation and agricultural research outcomes.

One group that has already benefitted from the service is the Australasian Wildlife Genomics Group, School of Life and Environmental Sciences at the University of Sydney, where Postdoctoral Bioinformatician, Dr Kate Farquharson, said:

The Fgenesh++ service has helped us easily and efficiently annotate multiple diverse genomes to a high standard.

Fgenesh++ is installed on computational resources provided by the Pawsey Supercomputing Research Centre and supported by Bioplatforms Australia, which is enabled by NCRIS. 

Learn more about how you can apply to access BioCommons’ Australian Fgenesh++ Service.

Our Genome Annotation Infrastructure Roadmap for Australia presents a national vision for shared national infrastructure that will help researchers undertake genome annotation. It was developed through our engagement with a broad range of Australian researchers working across a wide variety of taxa. If you would like to join in the conversation, let us know what else is required and also receive updates on new services coming online, please sign up to our google group.