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.

Building capability in the BioCommons team

Just as the breadth of our projects and services are evolving and expanding, so too is the BioCommons team. The past few months have seen people step into new roles and the welcome addition of some new faces.

Dr Jeff Christiansen has taken on the role of Deputy Director, Australian BioCommons. Jeff also continues as Associate Director: Engagements and Operations, so he will interface with key individuals and organisations nationally and internationally to develop and sustain BioCommons programs while working closely with the Operations and Research Community Engagement teams.

Dr Christina Hall has stepped up into the new role of Associate Director: Training and Communications. In recognition of the pivotal role that training plays in BioCommons’ outreach and the increasing importance and complexity of communicating our activities, Christina has been welcomed into the BioCommons leadership team.

Dr Farah Khan has joined BioCommons as Scientific Business Analyst. Hosted by QCIF and based at Melbourne Bioinformatics, Farah will assist the Research Community Engagement team to distil the requirements of omics researchers, find actionable solutions and ultimately support researchers to deliver their best research. Farah has a background in open science, genomics and computational bioinformatics and comes to us with an outstanding reputation for methodical and analytical approaches to documenting global community challenges for bioinformatics workflows.

BioCommons recently welcomed Gavin Graham as the Software and Platforms Service Manager, now hosted by QCIF in Brisbane. Gavin’s role is critical for ensuring a high quality researcher experience for our services such as Galaxy Australia, Apollo and Fgenesh++. He is tasked with ensuring that they are robust, stable, available and sufficiently resourced. Gavin brings 10+ years of experience working in IT management and bioinformatics in the university and private sectors.

Dr Ziad Al Bkhetan is the BioCommons’ new Bioinformatics Application Specialist. Ziad’s background in software engineering and bioinformatics have seen him applying computational methods to machine learning and genomics challenges in previous roles. Based in Melbourne, Ziad will coordinate and support communities to use software and methods and access HPC infrastructure to produce valuable data sets as part of the ABLeS program.

Check out our Team page to see the breadth of skills we now have spread across five Australian states in our Hub team.

Improve visibility of research software for career advancement

The Australian BioCommons, ABACBS and the ARDC Software Program recently co-hosted a wide-ranging panel discussion, Improve visibility of research software for career advancement.

Our MC and panellists, A/Prof Denis Bauer (CSIRO), A/Prof Kim-Anh Lê Cao (The University of Melbourne), Dr Sonika Tyagi (Monash University), Mr Fred Jaya (University of Sydney) and Professor Gordon Smyth, (WEHI) shared their experiences of developing, sharing code and software at various stages of their careers. Offering tips for getting started with sharing your own code and software, the suggested ways in which these activities can be better supported and sustained. Catch up by watching the recording and explore the resulting crowd-sourced list of resources on code review, software maintenance, registries and citations collected during the lively chat discussion.

Research software is both an essential part of doing research, and an important (but undervalued) research output. The Australian Research Data Commons (ARDC) has a National Research Software Agenda that describes how we can work together to See, Shape and Sustain research software. The goal is to lift recognition of research software to that of a first-class research output and to ensure that it is well-shaped and sustained and BioCommons backs #ResearchSoftwareAU whenever we can!

BioCommons’ Dr Johan Gustafsson, is co-leading the new Visible Research Software Interest Group along with Dr Paula Andrea Martinez (ARDC) and Dr Vanessa Crosby (University of New South Wales). It’s a focal point for the community to come together to jump-start coordinated activities to improve the visibility of research software, recognise authors of research software and improve software sustainability that started with the research software community’s wish to share information and resources. 

Watch the panel discussion video to learn how to Improve visibility of research software for career advancement.

AlphaFold now available in Galaxy

It seems the whole world is talking about AlphaFold, the AI system that predicts a protein’s 3D structure from its amino acid sequence that achieves accuracy comparable with real-life experiments. There was much fanfare last year when DeepMind published the scientific paper and source code that explained their innovative system.

In partnership with EMBL’s European Bioinformatics Institute (EMBL-EBI) the predictions for the shape of every single protein in the human body, as well as for the proteins of 20 other important organisms were made freely available to the scientific community.

Understanding a protein’s structure helps us to understand their function, and is traditionally achieved through slow, laborious experimentation. Painstaking effort over many years has determined the structures of around 100,000 unique proteins, but this represents just a tiny fraction of the billions of known protein sequences. Using computational approaches to enable large-scale structural bioinformatics to predict protein structures now promises to fast track our understanding of protein structure.

The team at Galaxy Australia saw an opportunity to further democratise access to this useful tool by making AlphaFold 2.0 available in Galaxy. Galaxy Australia provides Australian researchers access to a rich catalogue of computational resources and now includes the GPU clusters required to power AlphaFold 2.0. Life scientists can now easily visualise the consequences of DNA variants at the protein level, accelerating understanding of protein-protein interactions, activation or inhibition studies and drug design as examples.

It was an ambitious and technically challenging task, made possible through the work of multiple people around Australia, and indeed the world. While Galaxy Australia Developers and Admins laboured away to make the specific hardware, reference data and environment setup work together, Galaxy EU provided the necessary GPU-enabled development machine to test the approach. This technical triumph means that AlphaFold 2.0 is now available for installation on all Galaxy services globally, via the Galaxy toolshed. If you are interested in the technical details, you can visit the development repository.

Thanks to Galaxy Australia, the new Australian AlphaFold Service is now taking amino acid sequence uploads. All the set-up and provisioning of underlying GPU infrastructure are taken care of, so researchers can focus on generating the protein 3D structure itself. The service is currently available to early adopters for testing and benchmarking. If you think you might have a great research application for using AlphaFold in Galaxy Australia, please submit an expression of interest.

The work forms part of an exciting broader project to expand Galaxy Australia to utilise commercial cloud resources, enabling massive scale-up of the platform and access to specialised resources. It is expected that Galaxy Australia’s AlphaFold jobs will run soon on the Azure Cloud thanks to an Australian BioCommons collaboration with BizData and Microsoft Azure.

Stay tuned for upcoming stories explaining how early adopters are using the new resource on Galaxy Australia. If you are excited that your research questions can be answered by using the new Australian AlphaFold Service, let Galaxy Australia know via this form.

Enhancing secure and responsible sharing of human genomics research data

Human genomics is one of the most active areas of cutting-edge life science research and generates enormous amounts of data. Helping us to understand the genetic basis for health, the human genome also offers clues about the causes, detection, diagnosis and treatment of diseases. Meaningful information comes from comparing an individual’s genomic information to a bigger group of genomes with known characteristics. The insights become more powerful when comparisons are made with larger numbers of individuals, which can sometimes be difficult with rare diseases and genetic variations.

Optimal results come from combining matching data from different studies undertaken in a range of places. Dispersed treasure troves of data need to be shared between researchers on a global scale, which requires the valuable information to be findable, searchable, shareable and able to be linked to analysis platforms.

Many Australian human genome sequencing and analysis efforts have developed in-house solutions to manage their research data. Different technologies have been used for storing genome data and they are described in different ways. When researchers find data they would like to use from another source, they encounter manual, bespoke and opaque systems to request access.

Despite wanting to share data, most Australian researchers have no convenient way to expose what they have or distribute the data to trusted colleagues. For those that try, the task of sharing is complicated and often restricted by different laws in different jurisdictions. It’s not surprising, as there are few things more personal than genomic information, and the privacy of individuals should be protected. It is paramount that genomic data is used by researchers in a safe, ethical and secure way.

The capability to securely and responsibly share human genome research data nationally and internationally will be enhanced by the Australian BioCommons project “Global Technologies and Standards for Sharing Human Genome Research Data”, commonly known as the ‘Human Genomes Platform Project’. Experts in human genomics from many of Australia’s largest human genome sequencing and analysis efforts are working as part of a team that will deliver fundamental improvements in data management and drive access to new capabilities that will enable new science from valuable genomic data.

With co-investment from the Australian Research Data Commons and Bioplatforms Australia, BioCommons brought together valuable staffing contributions from ZERO Childhood Cancer, Children’s Cancer Institute, Australian Access Federation, University of Melbourne Centre for Cancer Research, Australian Genomics, National Computational Infrastructure, The Garvan Institute of Medical Research and QIMR Berghofer Medical Research Institute for this exciting new $3.3M collaborative project.

The large multidisciplinary team will investigate international best practice technologies for human genome data sharing, and deploy them for the first time in Australia in the form of a ‘services toolbox’ for use by the organisations that hold most human genomes collected for research in Australia. The toolbox will build on existing standards drawn up by respected initiatives including the Global Alliance for Genomic Health (GA4GH) and ELIXIR.

Critically, the project will facilitate ongoing adoption and deployment of these technologies at other organisations by establishing a working template for sharing widely.

Some aspects of this work build on a previous BioCommons project. For an overview of this project you can watch the webinar Establishing Gen3 to enable better human genome data sharing in Australia.

Learn more about the specific aims of the Human Genomes Platform Project here.

The HGPP is an Australian BioCommons project with co-investment from the ARDC (https://doi.org/10.47486/PL032) and BPA, both supported by the Australian Government’s National Collaborative Research Investment Strategy (NCRIS) . It receives in-kind support from the AAF, CCI, Garvan Institute, NCI, QIMR Berghofer and UMCCR.