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.

Bioinformatics and data skills training communities

There are so many communities, forums and meetings full of excellent people doing great things while training researchers. Now that most have switched to online meetings we are grabbing on the opportunity to connect with specialised groups of experts from around the globe. Here are just a few groups we participate in that are related to life science training - please come along and get involved!

The Life Science Trainers group is a global community of practice for short-format training in the life sciences. The monthly Community Calls are conveniently held in two time zones and are a fun way to exchange ideas and experiences, offering new ways of thinking about and doing training. It is a diverse group that is open to all trainers who serve researchers and educators in the life sciences.

Find out more about LifeSciTrainers and join their Slack channel

EOSC-Life hosts a network interested in training, and has an ongoing series of virtual Remote Training events. BioCommons presented at their recent knowledge-exchange workshop on hosting hybrid events that was attended by nearly 70 participants from mostly European countries, but also others such as Australia and Argentina (snapshot of meeting above). It was a great opportunity to hear about other people's experiences of organising virtual events.

Learn more about EOSC-Life and sign up for their newsletter

The Carpentries teaches digital research and data skills to researchers. It is a global community of trainers and learners who share a passion for evidence-based teaching practices and peer learning. A new ARDC-coordinated Carpentries partnership between 10 universities and research institutions will give Australian research institutions of all sizes access to two-day Carpentries instructor training at a reduced rate in 2022. Carpentry Connect Australia is a community networking event for new instructors and people interested in joining the Carpentries community in Australia.

Register for the 3 Nov 2021 free online Carpentry Connect event

There are a couple of Slack-based Australian groups that BioCommons participates in that might be of interest to bioinformatics trainers. The ENRICH CoP slack channel is for people interested in supporting and upskilling Australian researchers. The new Bioinformatics and HPC CoP has active discussions and has already had their first online meetup.

Join the Bioinformatics & HPC CoP before the next meetup

The Global Organisation for Bioinformatics Learning, Education and Training (GOBLET) aims to unite, inspire and equip bioinformatics trainers worldwide. They are a supportive community with ongoing working group activities that meet up at conferences where possible. BioCommons presented at their online 10th anniversary celebrations and enjoyed the international networking opportunity.

Check out the GOBLET bioinformatics training resources

Collaboration creates a new national registry of training events, materials and trainers

The Australian BioCommons training program has long benefitted from a close connection with ELIXIR Europe through its Training Platform. Our Bioinformatics Training Advisory Group draws members from Europe, the US and across Australia and resulting collaborations offer support and encouragement across continents. The impact of being able to draw on the experience of international peers is demonstrated by the imminent launch of a new training events and materials portal for Australasia based on ELIXIR’s TeSS.

Australian bioinformatics training events have been submitted to the international TeSS portal since 2017. Recognising the utility of a single registry that compiled bioinformatics events and materials and was searchable by location and topic, we advocated (then as EMBL-ABR) for its use by bioinformatics training providers around Australia. The Australian Bioinformatics and Computational Biology Society joined us in using TeSS for several years and both organisations displayed the TeSS portal on their websites. When the opportunity arose to share our experience outside of the bioinformatics training community, we connected ELIXIR and the data science training community.

At a BioCommons Bioinformatics Training Advisory Group meeting, discussions between members recognised that the ongoing challenges faced by Australians seeking data science and eResearch training could be addressed by the application of a platform like ELIXIR’s TeSS. BioCommons was invited to give an introduction to how we used TeSS at the ARDC Skills Summit 2020, and we connected a newly formed working group with our Advisory Group member and Co-lead of the ELIXIR Europe Training Platform, Dr Celia van Gelder, who provided key information about TeSS’s capabilities. Two of the Australian members of our Advisory Group, Ann Backhaus (Pawsey) and Melissa Burke (Australian BioCommons), ultimately helped form the working group that collaborated on the design and delivery of a training registry based on the codebase of TeSS.  Melissa has also continued to regularly contribute to the TeSS Club whose activities unite the international community to improve the training platform. 

I really think this is an excellent example of successful collaboration in the global training landscape. We are one community.

Dr Celia van Gelder
Co-lead ELIXIR Europe Training Platform
Australian BioCommons Training Advisory Group member 

The active working group with members from Australian Research Data Commons (ARDC), Australian BioCommons, Pawsey Supercomputing Research Centre, Intersect Australia, CSIRO, Deakin University, Sydney Informatics Hub - University of Sydney, National Computational Infrastructure, University of Newcastle, Federation University, Monash University, QCIF and the University of Queensland was convened by ARDC. They consulted with the TeSS Project Manager and Software Engineer, Chris Child, from ELIXIR-UK, and Pawsey and ARDC provided funding to bring in developer Nick May to deliver the tailor-made Digital Research Skills Australasia (DReSA). The extensions and customisations developed for DReSA are also feeding back into improving TeSS.

DReSA aims to make it easier for learners, trainers, and training providers to find digital research skills-focused educational events and resources in Australasia. This wonderful example of collaboration around a common challenge involving a large group of Australian organisations and ELIXIR is now ready for launch. We can’t wait to see BioCommons training listed there amongst the community’s events! The first iteration of DReSA is available online, and DReSA will be officially launched on 11 Oct 2021 at the eResearch Australasia 2021 conference session, A national approach to improve discoverability and accessibility of digital research skills training events, materials and trainers.

More information on the development and features of DReSA is available in ARDC’s launch announcement.

DReSA has received investments from the Pawsey Supercomputing Research Centre (Pawsey) and the Australian Research Data Commons (ARDC). Pawsey and ARDC are funded by the National Collaborative Research Infrastructure Strategy (NCRIS).

Maximising the potential of bioinformatics training materials through FAIRification

Biologists have an insatiable appetite for learning about bioinformatics approaches and methodologies, but in talking to the community we’ve realised that finding the right training events (or training materials) can be tricky.

This challenge is being faced the world over and the international bioinformatics training community has recognised that it is one we need to tackle in a coordinated way in order to deliver sustainable and scalable bioinformatics training. One of the ways that the international community is aiming to solve this problem is by making training opportunities and training materials Findable, Accessible, Interoperable and Reusable (FAIR).

A number of global bioinformatics training community leaders published 10 simple rules for making training materials FAIR last year and have since been meeting regularly to discuss the practicalities of FAIRifying training opportunities and materials and to share advice. Co-author and BioCommons’ Training and Communications Officer, Melissa Burke, has been actively participating in these discussions and applying the principles to BioCommons training and materials. Melissa also co-leads a Task Force in the ELIXIR FAIR Training Focus Group. 

To help Australians connect with bioinformatics training opportunities we list our upcoming webinars and workshops on our website and in ELIXIR’s TeSS portal (a global registry of life science training events and resources), alongside a huge variety of other bioinformatics training. We’ve also encouraged other organisations like the Australian Bioinformatics and Computational Biology Society (ABACBS) to do the same.

More recently we’ve started listing detailed descriptions and training materials, like slides and handouts, from our recent events in the Australian BioCommons training Zenodo archive. This forms a stable digital archive of freely available material so that you can refer back to them after the event, use them for self-paced study or even as inspiration or foundations for your own training events (all material is licensed to allow free re-use). Our webinars are also available on the Australian BioCommons YouTube channel for you to watch at anytime.

This approach is proving to be particularly popular with lots of downloads from the BioCommons training Zenodo archive and views of the materials already. We’re also seeing added advantages of improved recognition for the effort our trainers put into developing and delivering training (supported through the use of ORCID identifiers), as well as new collaborations and ideas for future training events.  

These activities have coincided with conversations with the wider digital research skills community within Australia who have experienced similar challenges with the discoverability of their training offerings. Happily BioCommons has been able to connect the Australian eResearch digital skills community with the developers of ELIXIR’s TeSS platform and contribute to the development of a data science and eResearch training portal, Digital Research Skills Australasia (DReSA), which will provide a new way for Australians to find and access the training they need. 

Please join us on 12 Oct as we share our insights into Maximising the potential of training materials through FAIRification at eResearch Australasia 2021. Alternatively you can watch a recording of this presentation on our YouTube Channel.