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.

Hear about our latest developments at eResearch Australasia 2021

Many of the Australian BioCommons team and partners working on our projects will be presenting at the next eResearch conference from 11-15 Oct 2021. The full program is now available, but here’s a snapshot of ways to hear about our ongoing developments:

11 Oct 2021 A national approach to improve discoverability and accessibility of digital research skills training events, materials and trainers (Birds of a Feather session), Ann Backhaus, Melissa Burke, Kathryn Unsworth, Anastasios Papaioannou, Darya Vanichkina, Kay Steel, Mark Crowe, Mortaza Rezae, Jon Symon

11 Oct 2021 Supporting data life cycles at the macro scale (Talk), Steve Quenette, Ai Lin Soo, Rhys Francis, Carina Kemp, Adrian Burton, Carmel Walsh, Max Wilkinson

12 Oct 2021 Maximising the potential of training materials through FAIRification (Talk), Melissa Burke, Jeff Christiansen, Christina Hall

13 Oct 2021 Galaxy Australia – a strengthened national life science service that engages globally (Talk), Gareth Price, Simon Gladman, Nigel Ward, Steven Manos, Rhys Francis, Andrew Lonie

13 Oct 2021 Scalable bioinformatics workflows for growing ‘-omics’ datasets on National Collaborative Research Infrastructure Strategy facilities (Talk), Tracy Chew, Georgina Samaha, Ove J. R. Gustafsson, Sarah Beecroft, Marco De La Pierre, Nigel Ward, Rosemarie Sadsad

13 Oct 2021 The Australian Apollo Service: establishing a national service – the process that got us there (Talk), Tiff Nelson, Jeff Christiansen, Justin Lee, Gareth Price, Nick Rhodes, Madeline Bassetti, Alejandro Bulgaris, Mike W C Thang, Cameron Hyde, Mark Gray, Melissa Burke, Christina Hall, Brian Davis, Steven Manos, Andrew Lonie, Nigel Ward, Dominique Gorse

15 Oct 2021 Australian BioCommons ToolFinder: discovery of bioinformatics software in an Australian infrastructure context (Talk), Ove Gustafsson, Jeffrey Christiansen, Tiffanie Nelson, Nigel Ward, Dale Roberts, Brian Davis, Marco De La Pierre, Tracy Chew, Dominique Gorse, Gareth Price, Andrew Lonie

Launching the new Australian Apollo Service for collaborative genome annotation

Australian BioCommons is thrilled to announce the launch of the Australian Apollo Service in partnership with QCIF and Pawsey Supercomputing Research Centre. This new service offers access to the popular tool, Apollo, which facilitates real-time collaborative curation and genome annotation editing, along with a valuable layer of IT support. The Australian Apollo Service allows researchers to focus on the genome annotation curation itself by taking care of all the system administration and hosting customised, local instances of Apollo.

Community roadmaps developed together with the Genome Annotation and Genome Assembly Communities highlighted the local need for access to Apollo. Many researchers who undertake genome annotation work identified Apollo as essential to their research as it allows them to collaboratively improve genome annotations that are the product of automated annotation tools or pipelines. But these researchers faced significant challenges in using this software as the overhead of deploying and managing an Apollo instance themselves was too high. 

Recognising this as a priority, Australian BioCommons has brought together partners at QCIF and Pawsey to build and deliver a service that is freely available to Australian-based research groups and research consortia. The complete system administration, build and deployment of the instance is done on behalf of researchers, with support provided through a help desk, user documentation and training events. The deployment of a full technology stack, long term hosting of data, maintenance updates and security are all covered by the Australian Apollo Service, providing customised, local instances of the Apollo software for individual genome projects.  

At our launch webinar, you’ll hear what’s possible from Dr Rahul Rane (CSIRO), Prof Sandie Degnan and Prof Bernie Degnan (University of Queensland) and Julia Voelker (Southern Cross University). The demonstration of what Apollo brings to these researchers’ genome annotation and curation workflows will be accompanied by an overview of what the Australian Apollo Service can offer from Dr Tiffanie Nelson (Australian BioCommons).

New users will be supported by a hands-on training workshop Refining genome annotations with Apollo in November led by experts in the Apollo tool and its use to support genome annotation, Dr Anthony Bretaudeau (French National Institute for Agriculture, Food, and Environment), Dr Helena Rasche (Erasmus Medical Center, The Netherlands) and Dr Sarah Williams (QCIF).

If you are interested in genome annotation, editing and curation, or you think that Apollo might be useful for your research, please join us for the webinar: Launching the new Apollo Service: collaborative genome annotation for Australian researchers on Wed 29 Sep, 2021 at 12:00 pm AEST.

BioCommons partner QCIF is offering the Apollo Portal service, and it is underpinned by computational resources provided by the Pawsey Supercomputing Research Centre. These efforts are supported by funding from the Queensland Government’s Research Infrastructure Co-investment Fund (RICF), Bioplatforms Australia (BPA) and Australian Research Data Commons (ARDC). BPA and ARDC are enabled by NCRIS.

Another global training success with the ‘SARS-CoV-2 Data Analysis and Monitoring’ workshop

Australian researchers recently took part in the international workshop, SARS-CoV-2 Data Analysis and Monitoring with Galaxy, thanks to the support of the Galaxy Australia team. 

Joining 750 registrants from 82 countries, local researchers participated in four days of training in SARS-CoV-2 data analysis and data management. Experts from Africa, Europe, the USA and Australia came together to offer 25 tutorials, 7 hours of pre-recorded videos (including lectures, demos and hands-on) and 6 hours of live Q&A sessions. 

Australian experts from QCIF, Melbourne Bioinformatics and Australian BioCommons volunteered to offer live assistance to attendees in our time zone. This opened up the possibility of supported asynchronous participation during our waking hours, with the option of tuning in to daily synchronous Q&A sessions, during which Australian attendees joined the rest of the community as it addressed questions from the international audience. Eighteen people took part from Australia, sharing the experience with a diverse array of students, clinicians, technicians, and senior researchers. During the workshop, the videos had 3200 views, with a total of 320 hours of watch time.

As with all Galaxy community events, this workshop fostered the principles of open data, open science and open infrastructure, which are also key aspects in the global public health challenges brought on by the pandemic. True to that philosophy, all the tutorials are now freely available in the Galaxy Training Network (GTN) and the recordings on the Galaxy Project YouTube channel.

The feedback from participants has been very positive and there are plans to offer the workshop again. Galaxy Australia regularly provides live support to asynchronous Galaxy workshops on a variety of topics, allowing their reach to become truly global. Why not join in next time? These training events are freely available to registrants anywhere in the world, with the materials shared publicly afterwards.

We are so appreciative of the worldwide community of instructors and helpers that make these massive global training opportunities possible!

Head to the Galaxy Europe blog if you would like to read the full report on the workshop outcomes. 

What to do when your bioinformatics outgrows your compute

Need to take your bioinformatics to the next level? Maybe you need to better understand the compute requirements for your bioinformatics workflows, or learn how to access compute that suits your needs as an Australian researcher?

You can now watch the recordings of the popular webinars 'Where to go when your bioinformatics outgrows your compute' and 'High performance bioinformatics: submitting your best NCMAS application' and consult the associated 'cheat sheet' to identify your next steps.

In time for the opening of applications for the National Computational Merit Allocation Scheme 2022, we partnered with Sydney Informatics Hub (SIH) to offer advice to help researchers find the compute their research needs. SIH were already offering tailored support to their University of Sydney researcher community, and were keen to share their expertise more broadly. We drew in our national research infrastructure provider partners to share tips on accessing compute including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey.

You can watch the recording of Where to go when your bioinformatics outgrows your compute and consult the accompanying list of Australian research computing contacts. This ‘cheat sheet’ has been uploaded along with all of the other files, materials and metadata to the Australian BioCommons Training Materials repository.

If you know you need specialised compute infrastructure to support your use of efficient, scalable workflows for your data intensive research, then the High performance bioinformatics: submitting your best NCMAS application webinar provides life science researchers with insights into what makes a strong NCMAS application. It focuses on the technical assessment, and how to design and present effective and efficient bioinformatic workflows for the various national compute facilities.

If you would like to read the supporting documents or attend an online information session about the National Computational Merit Allocation Scheme 2022 round, visit this NCI Help page.

Draft tea tree genome published by Southern Cross University team

A new genome assembly and annotation promises insights into the genetic foundations of economically valuable traits in tea tree (Melaleuca alternifolia). 

Given the therapeutic and cosmetic value of terpene-rich tea tree essential oil, the genetics and biochemistry of terpene biosynthesis have been studied extensively. The publication of the draft genome for M. alternifolia extends currently available resources to investigate the genome structure and gene family evolution, and will enable further comparative genomic studies in the Myrtaceae.

The work by Southern Cross University’s Julia Voelker, Mervyn Shepherd, and Ramil Mauleon, was reported this week in Gigabyte: A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species.

In completing their high-quality draft genome, the researchers made excellent use of national research infrastructure provided by Australian BioCommons. They are one of a small group of early adopters who have been intensively testing a soon-to-be-launched service which will offer fully subsidised access for Australian based researchers to the proprietary bioinformatics pipeline, Fgenesh++, to enable automated eukaryotic genome annotation. The case for access to Fgenesh++ was identified via consultations with the BioCommons Genome Annotation community, which were captured in our Genome Annotation Infrastructure Roadmap for Australia. The service will be provided by BioCommons and hosted by Pawsey Supercomputing Research Centre. The BUSCO analyses documented in the publication were run on the flagship BioCommons service, Galaxy Australia.

Based on the new assembly, curation of the terpene synthase gene family in tea tree continues. Using another BioCommons service that is about to be launched, the SCU group used the Australian Apollo Service to visualise gene prediction results and manually improve their gene models. You can hear more about this work at the upcoming webinar: Launching the new Apollo Service: collaborative genome annotation for Australian researchers.

All Australian researchers are invited to join our communities which are formed around different research methodologies. Join to have your voice heard when we document community challenges, and see your needs met as the BioCommons continues to roll out improvements and solutions in shared bioinformatics and bioscience research infrastructure.

This open genome release forms part of an ongoing collaboration between SCU and the Australian Tea Tree Industry Association

Let's do this Biohackathon together!

Are you interested in joining this year’s Biohackathon Europe from home? We are too, but we know the time zone clash is simply awful. Remote working has seen many of us grabbing more opportunities to participate in meetings and events across the globe. There are so many great things to do with international colleagues, but they often result in very late nights and early mornings.

In recognition of how draining and lonely this can be, we’d like to join forces with you to support each other during the late nights. Let us know if you register for the Biohackathon Europe and we'll provide snacks and a way to keep in touch when your eyelids are getting heavy.

Expand your bioinformatics community by meeting your international peers and working intensively on practical coding challenges. It's free to join and the project descriptions are available for you to chose from. Of particular interest to the BioCommons community: Project 33: Implementation, testing and training on reference genome assembly pipelines for the eukaryotic tree of life and Project 38: Single Cell Multi-Omics Analysis.

The event is 8-12 November in CEST timezone, and registration closes on 17 September.

So please sign up now and let us know if you're going!

New high memory computers fast-track insights into large genomes

Photo by Rod Long on Unsplash

Galaxy Australia’s new high memory servers have delivered an impressive leap forward for scientists with large datasets and computationally-intensive analyses. In a promising test of new infrastructure capacity, the genome of Australia’s national floral emblem, the Golden Wattle (Acacia pycnantha) was assembled this month on Galaxy Australia, demonstrating game-changing efficiency for the service.

To complete this massive task seamlessly in less than 24 hours vindicates the recent expansion to the data integration and analysis possibilities of the Galaxy Australia platform. The assembly tool, FLYE, was used to process 50GB of raw nanopore data - representing approximately one billion base pairs from the whole Acacia genome. 

Large and complex in comparison to something like a microbial genome, the plant genome was an ideal candidate to test previous limits. This type of analysis could take months using conventional institutional compute resources, and worse still, the job can sometimes be prone to failing at the end of the long processing time. Due to memory limitations, this type of analysis wasn’t previously supported by Galaxy Australia. 

The capacity upgrade came after capital investment from the Australian Research Data Commons (ARDC) and Australian BioCommons was made into the Melbourne node of the ARDC Nectar Research Cloud at the University of Melbourne. An equivalent investment into high memory servers at Galaxy Australia’s QCIF node will also come online this year.

Rapid genome assembly not only increases research productivity, but it also facilitates iterative pipeline optimisation and increases the opportunity to gain more insights quickly. Research becomes more reproducible when it’s possible to update an analysis with a new tool version, or tweak and repeat analyses at the request of a research partner or reviewer.

The tests were performed using unique and valuable data that has been years in the making. Researchers at the Royal Botanic Gardens Victoria have been compiling a Golden Wattle reference genome as part of a national consortium tasked with generating whole genome sequences of iconic Australian flora and fauna. Genomics for Australian Plants was initiated by Bioplatforms Australia in partnership with researchers from the Australian State and National Herbaria and Botanic Gardens, and will ultimately ensure that the Golden Wattle genome is sequenced, assembled and shared. 

David Cantrill, Executive Director Science, Royal Botanic Gardens Victoria, said, 

The genome of Golden Wattle will help us identify which genes are important using comparative genomics for Acacia species of conservation concern, and will boost biogeographic studies on widespread species. We want to identify the genes affecting traits of economic significance such as bioactive compounds or salinity resistance.

The testing of the new Galaxy Australia capability is just the beginning of a comprehensive program of work to ensure all researchers can utilise the new powerful machines. Running whole pipelines that include quality testing of input data, trying different tool usage on data subsets and submitting jobs with a range of different parameters will keep the Galaxy Australia team busy for some weeks. Testing various tools on other big data sets and optimising workflows will ensure that researchers around the country can soon bring their own large genomes and assemble them like never before.

The ARDC and Bioplatforms Australia are enabled by the Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS)