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.

A new member for our Training Cooperative

After delivering many successful events in 2021, the National Bioinformatics Training Cooperative is keen to welcome new participants. We are thrilled that the South Australian Genomics Centre will come onboard to contribute expertise and broaden our reach across Australia. We look forward to hosting many more participants from South Australia at these free training opportunities in the near future.

The South Australian Genomics Centre (SAGC) was established in 2020 to support research in South Australia, as well as nationally and internationally. The SAGC is a partnership between the South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Flinders University, The University of Adelaide, the Australian Genome Research Facility (AGRF), and the Australian Wine Research Institute (AWRI). Its establishment was supported by an investment of >$7 million, including $2 million from Bioplatforms Australia (BPA).

As well as providing a broad range of services including RNA sequencing, small RNA sequencing, exome and genome sequencing, epigenomics, metagenomics, and single cell genomics, the SAGC Bioinformatics Platform supports users of the facility in all areas of genomics including animal, plant, environmental, microbial, and human genomics.

Bioinformatics training events offered by SAGC have been popular with South Australian researchers, and we look forward to them becoming more involved in national activities via the Cooperative.

Virus research tips Galaxy Australia over 3 million jobs

The Galaxy Australia service is being chosen by large numbers of researchers from around Australia to complete their bioinformatics analyses. Rapid uptake of the service has seen millions of jobs submitted across a broad spectrum of critical research questions with hard-hitting outcomes for the real world.

Here we highlight the work of Dr Rhys Parry, who recently submitted the three millionth job to Galaxy Australia. Rhys uses Galaxy Australia extensively in his current role as a Postdoctoral Research Fellow in Professor Alexander Khromykh’s RNA Virology Lab in the School of Chemistry and Molecular Biosciences, University of Queensland.

Currently utilising Galaxy Australia for RNA-Seq analysis and assembly of SARS-CoV-2 genomes, Rhys has become a power user since he was first encouraged by his PhD supervisor, Professor Sassan Asgari, School of Biological Sciences, University of Queensland, to make use of Galaxy and the Galaxy training resources.

The Aedes aegypti (top) and Aedes albopictus mosquitoes (below) vector many pathogenic viruses to humans, but non-human viruses remain elusive. Bioinformatics tools from Galaxy Australia helped explore the virome of these mosquitoes. (Picture of mosquitoes by Ana L. Ramírez.)

For my PhD project I assembled close to 4000 RNA-Seq datasets from samples from all over the world - a task that would have been impossible without Galaxy Australia
— Rhys Parry

On the hunt for mosquito-borne viruses, Rhys undertook ‘Trinity’ de novo assembly of the transcriptomes of two medically important mosquito species, Aedes aegypti, the yellow fever mosquito and Aedes albopictus, the Asian tiger mosquito. These two mosquitoes vector significant viruses including Dengue, Zika and Yellow fever. The research not only improved our understanding of the microbiome and virome of these mosquito species, but discovered many novel viruses including one that was pathogenic to humans.

Recognising the value of Galaxy Australia beyond virus discovery and transcriptome assembly, Rhys has also used Galaxy for bacterial de novo assembly and RNA-Seq pipelines and annotation and small RNA mapping and analysis. 

For the past few years, my bioinformatics analyses have used Galaxy Australia extensively to avoid the expense of proprietary software and to allow for reproducible and modular pipelines
— Rhys Parry

Six publications resulting from this work have acknowledged the Galaxy Australia team for not only the maintenance and provision of essential computational resources, but also for the technical assistance and scientific advice that individual team members Dr Gareth Price and Dr Igor Makunin provide users of the Galaxy Australia service.

Parry, R., James, M. E., & Asgari, S. (2021). Uncovering the Worldwide Diversity and Evolution of the Virome of the Mosquitoes Aedes aegypti and Aedes albopictus. Microorganisms, 9(8), 1653. https://doi.org/10.3390/microorganisms9081653 

 Madhav, M., Parry, R., Morgan, J. A., James, P., & Asgari, S. (2020). Wolbachia endosymbiont of the horn fly (Haematobia irritans irritans): a Supergroup A strain with multiple horizontally acquired cytoplasmic incompatibility genes. Applied and environmental microbiology, 86(6), e02589-19. https://doi.org/10.1128/aem.02589-19 

Parry, R., Wille, M., Turnbull, O. M., Geoghegan, J. L., & Holmes, E. C. (2020). Divergent influenza-like viruses of amphibians and fish support an ancient evolutionary association. Viruses, 12(9), 1042. https://doi.org/10.3390/v12091042 

Bishop, C., Parry, R., & Asgari, S. (2020). Effect of Wolbachia wAlbB on a positive-sense RNA negev-like virus: A novel virus persistently infecting Aedes albopictus mosquitoes and cells. Journal of General Virology, 101(2), 216-225. https://doi.org/10.1099/jgv.0.001361 

Parry, R., Naccache, F., Ndiaye, E. H., Fall, G., Castelli, I., Lühken, R., ... & Becker, S. C. (2020). Identification and RNAi profile of a novel iflavirus infecting Senegalese Aedes vexans arabiensis mosquitoes. Viruses, 12(4), 440. https://doi.org/10.3390/v12040440 

Parry, R., & Asgari, S. (2019). Discovery of novel crustacean and cephalopod flaviviruses: insights into the evolution and circulation of flaviviruses between marine invertebrate and vertebrate hosts. Journal of virology, 93(14), e00432-19. https://doi.org/10.1128/JVI.00432-19

Some research presented here received funding through ARC grants DP190102048 and DP150101782 and a University of Queensland PhD scholarship.

The Australian Reference Genome Atlas (ARGA)

This blog post was first published by the Atlas of Living Australia on 19 Jan 2022 here

In an Australian first, our national research infrastructures are creating a new digital atlas to allow researchers to easily discover and work with genomic data

To consolidate Australia’s genomic data and make it available for researchers to use, the Atlas of Living Australia, Bioplatforms Australia, Australian BioCommons and Australian Research Data Commons (ARDC) funded via the Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS) are collaborating on ARGA, the Australian Reference Genome Atlas.

The new genomic atlas will mean that researchers can easily discover and access genomic data for Australian species in one place.

The endangered Tasmanian Devil (Sarcophilus harrisii). Image: Brett Vercoe (CC-BY-NC).

Genomics – hidden secrets of living things  

Genomic data – the genome and DNA data of an organism – helps us to understand the core traits of species. It helps us work out why some species are more resilient and adaptive to environmental changes such as climate change, drought and bushfire.​

Information about how species respond to these pressures is critical to biodiversity research and agriculture. For example, genomic data is used in agriculture to develop crop and livestock species that are more resilient and better adapted to drought and climate change. In ecology, researchers use genomics to identify species for captive breeding programs and repopulation planting that are more likely to recover after significant environmental change, such as that caused by bushfires.

Tree of life, showing the diversity of life on earth. The branches indicate how organisms are related to one another. Genomic techniques help scientists refine their understanding of these relationships. Source: https://www.nature.com/articles/nmicrobiol201648

Australian genomic data

Australia is home to a large number of native species, including 157,000 animals, plants and fungi, many of which are unique to the continent.​

With the growth of DNA sequencing capabilities, Australian researchers in universities, research organisations, as well as museums & herbaria have generated huge amounts of genomic data.

There is huge appetite to delve into the data and find out what genomic secrets our native species hold. Genomic data science is a fast growing and exciting field of science, and researchers need simple and rapid access to genomic data.

At the moment Australia’s genomic data for our flora, fauna and fungi species can reside across numerous international data repositories, museums or research labs, making it difficult to find and access and compare genomic data on Australian species. Some genomics databases were generated and stored using old technology and the data is no longer accessible.

A national atlas for Australian genomic data

The Australian Reference Genome Atlas will locate and aggregate descriptions of all relevant genomic data specific to Australian taxa in one place (e.g. genome assemblies, genome annotations, barcodes, raw data, other ‘omic’ data).

It will enable scientists to search these data by organism. For example, by taxonomic group (e.g. genus, species, subspecies), as well as by functional classification (e.g. drought/salt/fire tolerance, conservation status), and by geographical classification (e.g. location, altitude).

ARGA will facilitate comparative analysis of genomic data. Researchers will be able to download data for offline analysis, or analyse data in cloud platforms.

Project Partners

Leading NCRIS research infrastructures are collaborating to develop and operate ARGA. This exciting program will leverage the skills, combined knowledge, infrastructure, and extensive international scientific networks of the project collaborators.

Atlas of Living Australia (ALA) is Australia’s largest national biodiversity data infrastructure funded by the National Collaborative Research Infrastructure Strategy (NCRIS) and hosted by CSIRO. The ALA is the Australian node of the Global Biodiversity Information Facility (GBIF). 

Australian BioCommons is enhancing Australia’s digital life science research through world-class collaborative distributed infrastructure. The BioCommons is supported by Bioplatforms Australia.

Bioplatforms Australia is a non-profit organisation that supports Australian Life science research by investing in state-of-the-art infrastructure and expertise in genomics, proteomics, metabolomics and bioinformatics. This is made possible through investment funding provided by the Commonwealth Government National Collaborative Research Infrastructure Strategy (NCRIS).

Australian Research Data Commons (ARDC) enables the Australian research community and industry access to nationally significant, data intensive digital research infrastructure, platforms, skills and collections of high quality data. As a national research infrastructure provider, the ARDC facilitates partnerships to develop a coherent research environment that enables researchers to find, access, contribute to and effectively use services to maximise research quality and impact.

For more information, contact support@ala.org.au.

This blog post was first published by the Atlas of Living Australia on 19 Jan 2022 here

New systems established for easier management and sharing of human genome data

The Establishing Gen3 to enable better Human Genome Data sharing in Australia project has been completed as part of the BioCommons’ Human Genome Informatics Initiative. 

The project laid the necessary groundwork required for Zero Childhood Cancer (ZERO) and University of Melbourne Centre for Cancer Research (UMCCR) to establish systems for easier management and sharing of their human genome data holdings, and to also ensure that other Australian providers and institutions can easily deploy the same solution in the future.

Australian BioCommons brought together key partners, ZERO, UMCCR, Australian Access Federation and Melbourne Bioinformatics to explore the establishment of Gen3 technology in Australia. Gen3, an open source software suite, allows data to be received, managed, described, quality controlled, and shared with authorised or authenticated individuals, with data objects able to be stored over any number of private or public clouds. Gen3 has been used to underpin several very large international genomic datasets that collectively house and describe data derived from hundreds of thousands of human samples. 

The investigations by the national team discovered the Gen3 technology could be used to support virtual cohort assembly, create user facing (public) interfaces to enable querying of data held in each genome repository, and to ensure that common data dictionaries and agreed minimum information standards can be applied across different genome repositories. It also allowed for interfacing with secure S3 sequence file data storage used by each genomics data repository, either in AWS cloud or on-prem. 

At the end of this six month partnership, we were happy to conclude that the Gen3 technology was able to meet the project aims and Gen3 instances have now been successfully deployed at both the Children's Cancer Institute and UMCCR, to better enable their human genome data management. Work to further streamline the safe and ethical use of human genome data for research in Australia is currently continuing in our associated projects: Global Technologies and Standards for Sharing Human Genome Research Data and Establishing a harmonised data environment for Australian Coronary Artery Disease (CAD) cohorts. 

If you’d like to find out more, the UMCCR and ZERO project teams will be sharing their experiences in establishing Gen3 instances in a webinar on 16 February 2022. You will hear about the challenges and opportunities that have arisen through this Australian BioCommons project while getting a demonstration of the capabilities of Gen3 and how it can support the management of human genome data for research purposes. 

Register now for the Establishing Gen3 to enable better human genome data sharing in Australia. 

Leveraging Galaxy Australia to teach proteomics

The complete set of proteins expressed by a living organism is known as its proteome. Studying the proteome is vital to being able to understand the role of proteins within an organism and how they react to changes in their environment. It can include evaluating how changes might relate to outcomes like a particular condition, disease, or pharmaceutical treatment. The study of proteomes - proteomics - involves the analysis of all proteins, including their composition, structure, modifications, location and functions. Heavily reliant on mass spectrometry, proprietary software is commonly used to turn output data into valuable insights. This can be an impediment for newcomers, who need well designed training materials that are simple and specific for the software they will use in the lab once they learn proteomics techniques and tools. 

Dr Matt Padula from the University of Technology Sydney (UTS), is a Senior Lecturer at their School of Life Sciences, and Director of the UTS Proteomics Core Facility, a facility responsible for providing the technical support and instrumentation to study proteomics. At the recent Biocommons showcase, Dr Padula shared his experience using Galaxy Australia and how it simplifies how he teaches proteomics.   

‘When it comes to actually training students in proteomics you have to develop a whole lot of materials that are specific for certain pipelines and then along comes Galaxy… Galaxy has made life a little bit simpler’ – Matt

There are a number of difficulties when it comes to teaching students proteomics. Firstly, access to proprietary software is a real problem when teaching large numbers of students. To add to the challenge, many university desktops aren’t powerful enough to run the programs smoothly, often resulting in analyses taking several days. To tackle these challenges, Matt turned to MaxQuant - an open source proteomics software designed to analyse large mass spectrometric data sets. While it requires no proprietary licence, MaxQuant’s desktop version still takes considerable time to process, while also being complicated with the setting of different searches and parameters proved problematic for students.

Matt began using MaxQuant through Galaxy Australia because it removes the need for a super powerful desktop and potentially messy software installations, simplifies analysis, and can be run from anywhere, allowing for easier remote learning and access. When using the tool through Galaxy Australia, your hard drive isn’t filled with unnecessary input or output files, and workflow creations are able to continue well into the night without interruption.

For Matt, choosing to use MaxQuant for his analysis and teachings has taken the complexity out of setting up searches, and the abundance of training materials on offer means he can simply direct students over to the Galaxy Training Network website. The tutorials have come in handy for both Matt and his students:

‘I use the excellent online Galaxy tutorials to guide me in the creation of a workflow, which I can just save and call it up when I need it’ - Matt

Matt also made use of Galaxy’s new internal Training Infrastructure as a Service (TIaaS). Providing Matt with clear and live insights into the progress of concurrent tasks, it facilitated tailored support of individual students. TIaaS also allowed the administrators of Galaxy Australia to anonymously monitor the training event and fine-tune any resourcing required to provide the students with the best experience possible. The service will soon be rolled out for use by anyone interested in using Galaxy Australia for their training. 

In addition to providing tools, workflows and training infrastructure, Galaxy also comes with an active community. For proteomics, the Galaxy-P community supports a multi-omics platform that provides integrative analysis and promotes collaboration. The supportive communities are made up of global partners with diverse backgrounds and perspectives, who are extremely passionate about open-source research. They are crucial in creating a supportive and engaging environment that stimulates research and encourages training opportunities for its members. Learn more about Galaxy’s proteomics community or take advantage of the proteomics training materials on the Galaxy Training Network.

Dr Matt Padula at University of Technology Sydney

Local impact through international engagement with ELIXIR

Collaborative activities between Australian BioCommons and ELIXIR have expanded rapidly since the signing of the three year ELIXIR - Australian BioCommons Collaboration Strategy in 2020 to leverage the international synergies between the two research infrastructures. The interactions so far have been productive, friendly and insightful, and span an impressive breadth and depth of topics.

An active diary of BioCommons’ engagements with ELIXIR tracks progress and enhances connections between activities. BioCommons is now participating in a raft of international ELIXIR activities through our national network of partners, involving team members from Bioplatforms Australia, Pawsey, NCI, QCIF, SIH at the University of Sydney and Melbourne Bioinformatics at the University of Melbourne.

Collaboration takes place across a range of ELIXIR Platforms and Australian representation in ELIXIR Communities helps to develop standards, services and training within specific life science domains in both Europe and in Australia. From recurring fortnightly meetings of large communities, to spontaneous targeted discussions to exchange practical updates between individuals, the mode of interactions are as diverse as the topics. Here we cover just a few examples. 

Tools Platform and WorkflowHub Community

The ELIXIR Tool Platform helps researchers find and use computational tools by ensuring that they are properly described, packaged, benchmarked and included in an online registry with links to appropriate documentation and training. Connected to the work of the Tools Platform is WorkflowHub: a registry for scientific computational workflows. Like bio.tools, WorkflowHub promotes FAIR sharing. 

BioCommons is taking a leading role in these activities by integrating with the Tools Platform, establishing solutions to streamline deployment of tools and workflows, and assessing approaches for benchmarking. BioCommons now also offers ToolFinder and WorkflowFinder which integrates directly with bio.tools and WorkflowHub respectively. The community can access these services to discover what bioinformatics tools are available on Australian infrastructures, along with the workflows that have been designed by the BioCommons & its partners and tested on these same infrastructures. 

Sustainability of services underpins these activities as highlighted by a lively, BioCommons-ELIXIR jointly-convened Knowledge-sharing workshop on the design and operation of national- and international-scale bioinformatics services at this year’s ELIXIR All Hands meeting.  

Training 

Training is a core element of enabling scientists to use tools and services to achieve their best research. The BioCommons Training Team and the ELIXIR Training Platform have much shared experience in this area. Meeting regularly to swap ideas and identify common training needs, we collaborate to bring training opportunities to Australian and European audiences (time zones permitting!). ELIXIR Training Platform members are represented on the BioCommons Training Advisory Group, and BioCommons also participates in the development of methods and best practice for sharing (FAIR) training materials. Our close connections have recently supported the creation of a new national registry of training events, materials and trainers for the Australian eResearch community, DReSA which is in turn feeding back into the development of ELIXIR’s TeSS Training Portal. 

Galaxy 

Galaxy is an international, community driven effort to make it easier for biologists to analyse their data without the need for programming skills. There are long established ties and connections between the Galaxy EU, US and AU communities who constantly improve the Galaxy platform by developing and sharing new tools, workflows and training.

Over the past two years the global Galaxy community has worked together to develop and deliver truly international and interactive training events. The GTN Smörgåsbord: a global Galaxy course and SARS-CoV-2 Data Analysis and Monitoring workshop have simultaneously trained thousands of researchers across the world and exemplify the collaborative nature of the Galaxy community.

BioCommons team members attend the regular ELIXIR Galaxy community meetings, sit on the Galaxy Executive Board and other governing committees as well as maintain the very popular Galaxy Australia service.

Whether through technical deep dives and the sharing of expertise, or providing alternate use cases and unique perspectives, the ability to connect directly with ELIXIR members is levelling up BioCommons’ impact and is having a positive influence on the direction and outcomes of many ELIXIR projects. If you would like to meet some of our ELIXIR peers who are actively involved in BioCommons collaborations, please join us for their presentations at the BioCommons Showcase 2021.