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)

Australian user community growth and infrastructure developments highlighted at global Galaxy conference

The Galaxy Australia team has just returned from the Global Galaxy Conference (GCC) - held virtually again this year - where they joined scientists, administrators and developers from more than 55 countries to share knowledge, skills and expertise in the two-week collaboration fest, training event and conference.

Simon Gladman and Gareth Price represented Galaxy Australia on the GCC Organising Committee and the team was well represented amongst the delegates. The team took the opportunity to highlight the rapid growth of the Galaxy Australia service with talks and posters featuring stories of how Galaxy Australia is responding to community needs and supporting skills development via the integration of new tools and workflows, especially those associated with large genomic data sets. They also took the community behind the scenes to see how recent infrastructure changes, including the move to AARNet and integration with CloudStor, are supporting the growth in demand for Galaxy Australia services, improving data transfer and allowing planning for the long term sustainability and reliability of the service. 

Training was also a highlight of the event with the Galaxy Australia team supporting those in Australian time zones to join the global training event and leading training in the admin track. Of course, the Galaxy Australia team itself continues to grow and the conference was a fantastic opportunity for newer team members Cameron Hyde (USC/QCIF), Grace Hall (Melbourne Bioinformatics), Madeline Basetti (QCIF) to undertake training to increase capacity and capabilities for Galaxy Australia.

Take a look at this blog post for highlights, recordings and training materials from the GCC.

Galaxy Australia course at University of Cambridge

Biologists and wet-lab scientists from the University of Cambridge have just completed a two day introduction to next-generation sequencing taught by Dr Gareth Price. As the Service Manager of Galaxy Australia, Gareth was once again invited to lead the online live subject ‘Next Generation Sequencing Platforms and Bioinformatics Analysis’ from his home base at QCIF.

Postgraduate students and staff from the Department of Genetics at the University of Cambridge were introduced to next generation sequencing technologies (NGS) and how they work, providers, common bioinformatics workflows, standardised file types, and sequence data quality control. They used the open, web-based platform for data-intensive life science research - Galaxy - that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses. The hands-on practicals in Galaxy explored sequencing quality control, before and after removal of low quality samples and concluded with how this data pipes into gene expression studies, variant calling and genome assemblies.

Gareth enjoys helping the graduate students, postdocs and staff members from the University of Cambridge who attend the course, and it’s the second time he has been invited to share his knowledge with a class of 30 students. Participation in global events by the Galaxy Australia team is rapidly increasing as borders become less of an impediment to international scientific projects. The majority of Gareth’s time is spent enabling life science research at many university departments around Australia by training and supporting bioscientists in their use of Galaxy Australia.

For further information about this University of Cambridge bioinformatics training event, read the Next Generation Sequencing Platforms and Bioinformatics Analysis description.

BioCommons presents: How to build national bioinformatics services

Earlier this month, BioCommons led the international 'Knowledge-sharing workshop on the design and operation of national- and international-scale bioinformatics services' as part of the ELIXIR All Hands 2021 meeting.

Bringing our experience in the development and operation of targeted infrastructure, platforms and services for bioinformatics, the BioCommons team and over 100 members of ELIXIR nodes came together to discuss shared ambitions, challenges and successes. The Australian perspective of nurturing the evolution of ‘grass roots’ and best efforts research infrastructure, to robust, highly available, supported and trusted services was presented. The BioCommons' collaborative approach that prioritises strong engagement with end-user and infrastructure operator communities was offered as a valuable path to understanding the research community's needs, helping direct the deployment and resourcing of appropriate infrastructure to maximise impact.

Excellent case studies were also presented from the ELIXIR Hub and nodes in Belgium, France and Spain. Capitalising on having so many knowledgable and powerful people engaged in the session, BioCommons took the opportunity to raise some big and difficult questions about funding sustainability at the national and international levels. With lots of references to keeping pace with emerging requirements and better demonstrating impact the sometimes contentious discussions ran the workshop overtime and generated 15 pages of notes! The workshop sparked plenty of new ideas and leads and we were thrilled with the response. 

BioCommons also showcased some of the work that Galaxy Australia and BioCommons are undertaking at the 'Strengthening the integration of Galaxy in the Tools Ecosystem' workshop, and participated in a raft of other discussions at workshops and talks across the ELIXIR All Hands meeting. The virtual event was held 1-11 June 2021 during our evenings in Australia. We were privileged to be invited to come together with the ELIXIR community in recognition of our collaborative partnership on many projects.