GVL creates connections across the Tasman

Last month the GVL was trialled by colleagues in New Zealand (NZ) who were interested in its use for both research and training in bioinformatics. Aleksandra Pawlik, Research Community Manager, New Zealand eScience Infrastructure, wrote afterwards:

We’re ending the first of the scheduled training workshops and indeed it was a great idea. GVL removes all the headache of setting things up but is also an infrastructure that (hopefully) will become available and prevalent among many researchers. I am saying that as from my experience in teaching computational skills to researchers, I know that it is essential to teach people tools that they can carry on using. Therefore usually Virtual Machines or ad-hoc cloud set ups are not ideal. They are available at the workshop but then researchers have to use whatever their organisations offer them.

This opportunity arose from an information exchange our Nectar colleagues were having with their NZ counterparts who are responsible for meeting the infrastructure needs of the New Zealand Government’s new national genomics initiative (Genomics Aotearoa, NZ$35M over 7 years). It is being hosted by the University of Otago, and involves a number of NZ universities and Crown Research Institutes. Genomics Aotearoa aims to put in place key genomics and bioinformatics infrastructure to underpin research exemplars across three themes: Health, Environment and Primary Production. An important component of this work involves the provision of a national genomics computing platform and for that they were keen to assess the GVL environment for genomics training and analysis activities.

Thanks to all involved in making this trial a success,

Assoc Prof Michael Black, Department of Biochemistry, University of Otago
Dr Michelle Barker, Deputy Director, Research Software Infrastructure, Nectar
Prof Glenn Moloney, Director, Nectar
Dr Paul Coddington, Deputy Director, Research Platforms, Nectar
Dr Aleksandra Pawlik, Research Community Manager, New Zealand eScience Infrastructure
Assoc Prof Andrew Lonie, Director, Melbourne Bioinformatics & EMBL-ABR
Mr Simon Gladman, GVL Lead, Melbourne Bioinformatics
Mr Nick Jones, Director, eScience NZ Infrastructure
Dr Elizabeth Permina, Bioinformatician, Otago Genomics and Bioinformatics Facility, Health Sciences, University of Otago
Prof Peter Dearden, Director, Director, Genetics Otago
Prof Cris Print, School of Medical Sciences, University of Auckland and co-lead bioinformatics, Genetics Otago.

We look forward to greater collaboration in the development of shared training resources for both our communities.

Nectar Virtual Labs deliver research impact

2 November 2017

In a Victoria University report published this week which set about measuring the return on investment on Australia’s Virtual Laboratories (VLs), which provide digital interfaces, tools and data to online research communities, it has been reported that they are generating a return on investment of up to 138 times their cost.  

Estimating the value and impact of Nectar Virtual Laboratories, written by the Victoria Institute of Strategic Economic Studies for the National eResearch Collaboration Tools and Resources project (Nectar), studied three Nectar-supported VLs across different disciplines, including the Genomics Virtual Laboratory hosted at Melbourne Bioinformatics.

Five methods of value measurement were used, including the impact the VLs have on research and how much users would be willing to pay for the service if it did not already exist.

The return on investment varies depending on the metric and the associated method of calculation, however the report has found that return on investment (ROI) is at least double the investment for every measure of each of the VLs studied, indicating the services have a significant economic and user impact. By one measure the value of the VL was over 100 times the cost of investment.

Go to full story at Nectar news.

Bioconda, simplifying software installation for bioinformaticians and life scientists

25 October 2017

Thanks to the global efforts of over 250 contributors, including our own Simon Gladman, bioinformaticians and life scientists now have access to Bioconda, a software-package building and management system designed for bioinformatics. This work is now documented at BioRxiv.





A common problem in computing and data science especially – known as ‘dependency hell’ –  occurs when you try to install software you want to run and it’s not compatible with your operating systems, versions, system set-ups etc. This creates an environment where the compilation requirements of the underlying systems are often competing with one another. In more mature fields of computer programming, packaging systems like Conda have been developed to overcome this problem: someone makes their software available using a ‘Conda recipe’ which describes the software, where to find it, what dependencies it needs both to build and run it and then some basic scripting to install it. The ‘recipe’ is then added to the Conda repository system where it is automatically ‘built’ into installable tool packages for various operating systems and hardware and then stored in a fully-supported, global repository.

Bioconda extends Conda into the life sciences and, in addition to making bioinformatics software installation much easier, improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without the need for administrative privileges.

It improves on other packaging systems by having an option to install tools in their own sandboxed environment so they don’t interfere with any other installed software. And every tool put into the repository automatically has a Docker container built for it.

Simon Gladman says,

The Bioconda project is very well organised with contributions to the repository via pull request and code review before merging. I’ve added roughly 30 packages to the Conda ecosystem (out of ~2500) since I started working with it, including our Microbial Genomics group’s most popular ones like Velvet Optimiser, Prokka and Snippy. I’ve also added tools I use a lot like Roary and Gubbins (Sanger Pathogens group). To progress the project we have held hackathons all over the world, the last one at the 2017 Galaxy conference in Montpellier.

About 2 years ago, the Galaxy project decided to experiment with using Conda and Bioconda as their preferred method of tool installation and they’ve now formally adopted it as standard. The latest version of Australia’s Genomics Virtual Laboratory (GVL) uses Bioconda to handle tool installations for Galaxy in the GVL and we’ve started working on ways to supply command line versions of the tools also.

An alternative packaging system Torsten Seemann contributes to is Homebrew Science. It pre-dates Bioconda and inspired many of the package formulae now employed in Bioconda.

January 2018 workshop

We have invited two Bioconda and Galaxy experts, Saskia Hiltemann (Erasmus University, The Netherlands) and Eric Rasche (Frieburg University, Germany) to run a Bioconda/Galaxy tool wrapping tutorial and workshop to help us build Australia’s capability in, and contributions to, this great community project.

Register your interest in this workshop with Christina Hall.


  • a repository of recipes hosted on GitHub
  • a build system that turns these recipes into conda packages
  • a repository of >2700 bioinformatics and other packages ready to use with ‘conda install’
  • over 250 contributors that add, modify, update and maintain the recipes

Follow the project on twitter: #bioconda

Watch 30 minute webinar from ELIXIR on Bioconda and Biocontainers by Björn Grüning (ELIXIR Germany).

Install your software using the conda system: after installing a conda system such as Miniconda, try ‘conda’ install <bioinformatics tool>.


Helping to make clinical genomics a reality for Victorian patients

For Melbourne Genomics, work is well underway towards the delivery of the first components of Victoria’s clinical system for genomics (‘GenoVic’). The work plan for this year sees the delivery of shared analysis and curation tools, data governance and clinical tools – paving the way for further elements of the system in 2018 and 2019.

Earlier this year Melbourne Bioinformatics was pleased to host and be part of the team which developed the benchmarks and was assessing two world-class curation tools to enable selection of the best tool for Victoria. This cutting-edge software will provide a streamlined, collaborative and easy-to-use way to interpret, share and store genomic information for clinical and research purposes.

We were very impressed with the team’s thoroughness and dedication to the task. Negotiations are now well underway with the selected vendor and you can read the full story at Melbourne Genomics.

Developing an Australian Biosciences Data Capability – October 2017 update

Within five years we estimate there will be more than 30,000 Australian researchers (and somewhere around 200,000 students) in agriculture, environment and health, spread across multiple roles: bioinformaticians, researchers who use and rely on bioinformatics-driven techniques, and those (the majority) who are still lab-focussed, perhaps using online resources to interpret research findings. These groups will have a variety of data needs and a variety of skills, and they will increasingly be interacting with both local and global resources.

So, questions arise such as: What infrastructure and activity is needed now to support all to do world-class science? Within our Australian funding context (in particular, the NCRIS Roadmap), what should we prioritise to give us the greatest leverage to access international resources and collaborations? How might we anticipate the kind of transformative science envisaged in a more data-intense future?

At the EMBL-ABR All Hands meeting held in Melbourne late in 2016, key people working across data, infrastructure and bioinformatics discussed the future needs for biosciences data capability (digital data, digital tools (software), cloud technologies and compute infrastructure) with members of the existing EMBL-ABR International Scientific Advisory Group (ISAG). Bioplatforms Australia then provided funding to contract Rhys Francis (author, NCRIS eResearch investment/super science plans (2007-10) and the draft eResearch Framework (2013-15)) to work with me to establish a framework, a plan, a process. Our ideas have since been ‘road tested’ at a large workshop with Queensland-based research leaders held in Brisbane earlier this month and more workshops are being planned for other States. We are also gathering a National Reference Group of high profile domain-specific researchers to act as guides and advocates. This group is meeting online in October in preparation for discussions with government in Canberra in late November. Concurrently we are testing our proposals with our experts on the EMBL-ABR ISAG.

We want to keep everyone informed about this process and this will generally be through the EMBL-ABR communication channels. So please sign up for EMBL-ABR news at www.embl-abr.org.au to get all updates.

If you wish to contribute to these discussions, or know how your institution or research is being represented in this process, please email alonie@nullunimelb.edu.au.

Hi-Plex: simple, low-cost, modular targeted DNA sequencing technology

Hi-Plex was developed by our Molecular Biologist, Assoc Prof Daniel Park and Computer Scientist, Dr Bernard Pope, co-leads of our Human Genomics Group at Melbourne Bioinformatics, to simplify processes and reduce costs on projects needing targeted sequencing of panels of genes across large numbers of specimens. It brings greater efficiency and accuracy to all such research projects – big and small.

Hi-Plex is suitable for an extensive range of clinical and research applications and is complemented by software for primer design and variant calling. It enables a PCR-based target-enrichment system, unrivalled in terms of simplicity, accuracy and cost.

Although per-base sequencing costs have decreased during recent years, library preparation for targeted massively parallel sequencing remains constrained by high reagent costs, limited design flexibility and protocol complexity. Hi-Plex addresses these limitations.

Hi-Plex is invaluable when looking into candidate cancer predisposition in large breast and colon cancer datasets involving thousands of samples.

It’s currently being applied in a nationwide study of approximately 10,000 women affected with breast/ovarian cancer who have tested negative for mutations in BRCA1 and BRCA2, known as the Brca Refined Analysis of Sequence Tests: Risk And Penetrance (BRA-STRAP). For this our team is using Hi-Plex to study a panel of breast cancer genes and candidate genes to determine prevalence and penetrance of mutations in the Australian population. This will facilitate translation of the panel testing approach into Familial Cancer Centres. The data can then be pooled with international data to build a more comprehensive, shared database to inform new genetic testing models for clinical practice worldwide.

University of Melbourne collaborator Prof Melissa Southey employs Hi-Plex in studies of prostate cancer susceptibility, with a current study involving in the order of 7,000 DNAs provided by participants of population based studies and it is also being used as part of a long term collaboration between Prof Southey and colleagues at the University of Pennsylvania.

Collaborator Assoc Prof Daniel Buchanan’s Oncogenomics laboratory at the University of Melbourne uses Hi-Plex to find associations between mutations in certain genes and predisposition for serrated polyposis, a type of colorectal cancer. Daniel will present this work in the Presidential Plenary Abstract Session at the forthcoming 2017 Collaborative Group of the Americas on Inherited Colorectal Cancer Annual Meeting in Orlando, Florida, USA.

In April 2016, HiPlex featured in a presentation by Sean Wen, part of the Breast Cancer Research team from Cancer Research, Malaysia, at the Global Breast Cancer Conference, one of the biggest conferences of its kind in Asia. Link to Sean’s slides here: Hi-Plex for High-Throughput Mutation Screening of BRCA1, BRCA2, TP53, and PALB2 in Breast and Ovarian Cancer Patients.

How it works:

Hi-Plex detects genetic variants and reports them in formats that work with complementary annotation tools.  In this way, variants can be broadly categorised according to their likely clinical significance. This is a typical Hi-Plex workflow:









While developed for large-scale cancer projects, Hi-Plex is now being demonstrated in diverse settings, such as the population genetics of non-model organism snails and crayfish.

Contact the Hi-Plex team for information and collaboration enquiries from tech transfer, reagent design, methods, data analysis, including bespoke analysis pipelines.


Related Journal References:

Park, D. J., Li, R., Lau, E., Georgeson, P., Nguyen-Dumont, T. & Pope, B. J. UNDR ROVER – a fast and accurate variant caller for targeted DNA sequencing. BMC Bioinformatics 17, 165 (2016).

Nguyen-Dumont, T., Hammet, F., Mahmoodi, M., Pope, B. J., Giles, G. G., Hopper, J. L., Southey, M. C. & Park, D. J. Abridged adapter primers increase the target scope of Hi-Plex. Biotechniques 58, 33–36 (2015).

Nguyen-Dumont, T., Mahmoodi, M., Hammet, F., Tran, T., Tsimiklis, H., Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Giles, G. G., Hopper, J. L., Australian Breast Cancer Family Registry, Southey, M. C. & Park, D. J. Hi-Plex targeted sequencing is effective using DNA derived from archival dried blood spots. Anal. Biochem. 470, 48–51 (2015).

Pope, B. J., Nguyen-Dumont, T., Hammet, F. & Park, D. J. ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets. Source Code Biol. Med. 9, 3 (2014).

Nguyen-Dumont, T., Pope, B. J., Hammet, F., Mahmoodi, M., Tsimiklis, H., Southey, M. C. & Park, D. J. Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing. Anal. Biochem. 442, 127–129 (2013).

Nguyen-Dumont, T., Teo, Z. L., Pope, B. J., Hammet, F., Mahmoodi, M., Tsimiklis, H., Sabbaghian, N., Tischkowitz, M., Foulkes, W. D., Kathleen Cuningham Foundation Consortium for research into Familial Breast cancer (kConFab), Giles, G. G., Hopper, J. L., Australian Breast Cancer Family Registry, Southey, M. C. & Park, D. J. Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2. BMC Med. Genomics 6, 48 (2013).

First Melbourne Genomics bursary awarded to MSc Bioinformatics student Ms Jia An Yu

University of Melbourne Master of Science (Bioinformatics) student Ms Jia An Yu, is a welcome addition to Melbourne’s Biomedical and Biosciences precinct. Jia An’s undergraduate training was in biology in China’s north east at Harbin Institute of Technology (HIT), a large multi-disciplinary, nationally-renowned university focussed on science, engineering and research. At HIT she developed an interest in where big data was taking the life sciences so she went looking for a relevant post-graduate degree.

Three things convinced Jia An to apply to this course: the University’s No. 1 ranking in Australia and its international ranking, Melbourne being one of the most liveable cities in the world and the unique structure of the course with streams for biology, mathematics and computer science undergraduates to learn from each other while not holding each other back.

Following a great start to the year, Melbourne Genomics have awarded Jia An a $5000 student bursary and this supports her study while she puts her new skills into one of their research projects. This one is led by Associate Professor Paul James, from the Royal Melbourne Hospital and Peter MacCallum Cancer Centre, and is aimed at developing a clinically oriented approach to whole genome data for inherited cardiac disorders. Read about Melbourne Genomics projects here. Other supervisors include Lavinia Gordon, Bioinformatics Manager at Australian Genome Research Facility and Lead Bioinformatician, Human Genomics Group, Melbourne Bioinformatics, Dr Bernard Pope.

Dr Pope said, “I know Jia An is keen to start applying her new skills. This is an excellent engagement model: Jia An gets to work on a real-life problem and Paul gets help to progress his important clinical work.”

Of the Master’s course, Jia An says: “Some students who enter the course with a biology background find the mathematics challenging, but I have found that the high standard of mathematics which I learned in China at HIT has really helped me to get the most out of this course. I am developing a unique set of skills which I know are in high-demand, so it is exciting to see where it will take me.”

MSc (Bioinformatics) information

Melbourne Genomics

Simon Gladman, Research Scientist specialising in microbial genomics, May-June UK tour, Blog #2

After arriving back at Melbourne Bioinformatics after 8 weeks of delivering training across Europe, here’s a list of my highlights of training and collaborating.

Blog 1

Blog 2: Elixir, CLIMB, Sanger and the Galaxy Community Conference

Collaborations with Elixir, Elixir Hub – Hinxton – 5-9th June and then elsewhere

I spent a few days hanging out with the awesome people at the Elixir hub at the Wellcome Trust Genome Campus in Hinxton. We spent quite some time working on some joint proposals for projects between Elixir and EMBL-ABR with Rafael Jiminez of Elixir Hub and Vicky Schneider of EMBL-ABR.

I also continued our discussions with the Victoria Dominguez de Angel of the French Elixir node and we came to an agreement for them to use the GVL and some NeCTAR resources to teach their national week long bioinformatics course in the week of July 3rd. Jessica Chung and Nuwan Goonasekera from Melbourne Bioinformatics were instrumental in the provisioning of this infrastructure. They were impressed with the GVL and what it offers them for bioinformatics training and analysis. The training course was a complete success and both the participants and teaching staff were enthusiastic about the GVL.

Work continues in the coming months to make the GVL available on the French Institute of Bioinformatics (IFB) cloud infrastructure for use by researchers all over France. I also spent some time discussing GVL options with Frederick Coppens and Björn Grüning of the Belgian and German Elixir nodes (respectively) and have agreed to make the GVL available on their Clouds. Björn will be implementing the availability in July 2017.

Genome Assembly Workshop at Cambridge University, Cambridge University Genetics Department – Downing Site, – 6th June

I was invited by Gabriella Rustici of the Genetics Department of Cambridge University to give a workshop to university staff on Genome Assembly, Annotation and Galaxy. The workshop was an entire day of hands on tutorials for genome assembly and annotation using the GVL infrastructure and training materials. The feedback from the participants was extremely positive and they all learned a lot of instantly applicable skills. Gabriella and Paul from the training department were very happy with the way the GVL training material works and engages the students. They are looking at the adoption of our materials and incorporating them into their ongoing training.

CLIMB Hack – Cardiff, Cardiff University – 12-16th June

I was invited by Tom Connor to visit Cardiff University which is one of the nodes of the UK CLIMB consortium. He also organised the CLIMB personnel from the other sites (Warwick, Birmingham and Swansea) to attend and make it a week long hackathon for their cloud infrastructure and machine images. Along with Radoslav Poplawski, Matt Bull, Tom, Nick Loman and Maciej Filocha, I made the new GVL 4.2 available on the CLIMB infrastructure, worked on more microbial training material, made more tools available to the wider community and taught some of the CLIMB staff to write ansible scripts for cloud resourcing, and tool recipes for Bioconda and Galaxy. We also found the time to visit the Swansea facility of CLIMB which was in a lovely place right on the beach (albeit a Welsh beach…) 

Sanger Research Centre

At the microbial hackathon in May, I organised to spend 3 days to a week at the Sanger Institute with the bioinformatics core, teaching staff how to use Bioconda and write tools for Galaxy. So I spent the week with Jaqueline Keen, Andrew Page and John Lees getting Sanger’s very useful tools into Bioconda, Biocontainers and Galaxy. By the end of the week we had put “Roary the pangenome pipeline”, “Gubbins – Genealogies Unbiased By recomBinations In Nucleotide Sequences” into Galaxy via Bioconda and made significant progress on many others including John Lees’ SEER bacterial GWAS software. As each tool was completed, it was incorporated into the GVL and currently training material is being produced for them. I also got to spend an evening in the very beautiful Saffron Walden (an old market town) just near the Wellcome Trust Campus. 

Galaxy Community Conference, Le Corum – Montpellier, France

I was lucky enough to catch the train from London down to Montpellier in France for the Galaxy Community Conference. This conference brings together Galaxy developers, users, trainers and communities together for 5 days of hacks, training and conference.

The schedule for the conference along with all the slides etc. can be found at: https://gcc2017.sched.com/

The first two days were called “Hack the Galaxy” and incorporated people from the broader Galaxy community working on the codebase, training material, user interface improvements, test and training data sets. I worked with some of the French participants on getting tools and materials into Galaxy. It was a lot of fun and it did improve my French!

Day 3 was a Training day. I taught two workshops and participated in a third. I taught de novo Genome Assembly for about 20 participants in the first session with assistance from Dan Blankenburg from the Galaxy Project.  I attended Metagenomic Analysis with Galaxy in the second session, then Nate Coraor, Dan Blankenburg, Martin Čech, Enis Afgan, John Chilton (all of the Galaxy Project) and I taught accelerated Advanced Galaxy Administration. This was taught with material we developed for the week long Galaxy Administration courses held in Salt Lake City and Melbourne in 2016/2017. It was a very busy day. The feedback from the workshops was very encouraging and the participants were again impressed with the quality of the materials we have developed here in Australia.

Days 4 and 5 were the conference itself. There were a lot of high quality and interesting talks presented by people from all over the world. I gave a talk on Galaxy Administration Training and had a well received poster on Data Library Manipulation in Galaxy.

Some of the highlights of the conference were:

    * Anton Nekrutenko and James Taylor of the Galaxy Project gave a wonderful keynote on the evolution of Galaxy

    * Dan Blankenburg and Jeremy Goecks of the Galaxy Project gave the Galaxy Community Update

    * Marius Van Den Beek from the Curie Institute presented a poster on Detecting somatic de-novo Transposable Element insertions with Galaxy

    * A hilarious lightning talk from Jim Johnson of Minnesota University titled “Improving your text life”

    * Peter Van Heusden of Cape Town University: “COMBAT: an integrated environment for Tuberculosis data analysis and surveillance”. 

Finally, it was announced that next year’s Galaxy conference will be co-located with the Bioinformatics Open Source Conference in Portland, Oregon.

And so my epic journey through the UK and France came to an end. I would really like to thank everyone I visited and who hosted me over the last 8 weeks. We did a lot of work and got a lot of things done for the good of bioinformatics in Australia and elsewhere. Special thanks to EMBL-ABR, Melbourne Bioinformatics, Cardiff University, the Galaxy Project and Elixir for funding the trip. Thanks also to Vicky Schneider of EMBL-ABR and Dave Clements for setting up the interactions. Thanks also to Madison Flannery (ex Melbourne Bioinformatics) who gave me a base to operate out of. 

Stay tuned for my next blog where I’ll run through all of the outcomes of these interactions and the ongoing collaborations that have resulted from my trip.

Dieter Bulach co-CI on NHMRC project investigating sources of Campylobacter in Australia

Funded in 2016, this three-year NHMRC partnership grant is led out of ANU by Assoc Prof Martyn Kirk, with collaborators from public agencies and institutions around Australia and New Zealand.


Campylobacter is a key cause of foodborne disease globally, with Australian rates of reported illness amongst the highest in the world. Critical elements of successful control programs overseas have included collaborative sharing of information among stakeholders, development of innovative genomic and epidemiological methods, and use of this information to develop interventions to reduce the incidence of illness. This collaborative project seeks to harness rapid advances in genomics, epidemiology and mathematical modelling to identify risks and reduce human illnesses from Campylobacter in Australia.

CIA: Martyn Kirk (ANU)

CIB: Kathryn Glass (ANU)

CIC: Nigel French (Massey)

CID: Mary Valcanis (Unimelb: Doherty/MDU)

CIE: Dieter Bulach (Unimelb: Melbourne Bioinformatics/Doherty)

CIF: Emily Fearnley (ANU)

CIG: Craig Shadbolt (NSW Food Authority)

CIH: Russell Stafford (Queensland Department of Health)

CII: John Bates (Queensland Department of Health)

CIJ: Mark Stevenson (Unimelb: Faculty of Veterinary and Agricultural Sciences) 


APP 1116294

First Funding Year



NHMRC Partnership Project

Project Title:

Understanding the sources of Campylobacter in Australia

Funding Period:

3 Years

Funds Awarded:


Administering Institution and its first named Chief Investigator (CI):

Institution: Australian National University

CI: Assoc Prof Martyn Kirk


Participating Institutions(s) and its/their first named Chief Investigator



Professor Nigel French

Massey University NZ

Mary Valcanis

The University of Melbourne

Dr Craig Shadbolt

NSW Food Authority

Dr Russell Stafford

Queensland Department of Health

Other Participating Institutions not contributing Chief Investigator

Hunter New England Health

NSW Ministry of Health

Victorian Department of Health and Human Services

Rural Industries Research and Development Corporation

Food Standards Australia New Zealand

Commonwealth Department of Health


Human Genomics Paper, May 2017: Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics

Recently in our Human Genomics group we have been reflecting on the complex problems which can arise when performance metrics of genetic variant effect prediction algorithms used in clinical genomics and research are confounded by circularity and error propagation. Our findings have now been published online: Mahmood, K., Jung, C.H., Philip, G., Georgeson, P., Chung, J., Pope, B. and Park, D.J., 2017. Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics. Human Genomics, 11:10 DOI 10.1186/s40246-017-0104-8.

Go to Human Genomics Group web page.

Simon Gladman, Research Scientist specialising in microbial genomics, May-June UK tour, Blog #1

As our Genomics Virtual Laboratory expert, Simon Gladman was invited by colleagues in the UK and EU to spend time over summer on some key bioinformatics problems and to share some Australian know-how. He has already covered a lot of territory. Here he gives the first of several updates to come:

17-19 May

Applied Bioinformatics and Public Health Microbiology (ABPHM)

Sanger Wellcome Trust Institute – Hinxton

ABPHM is a conference for bioinformaticians and biologists from the public health space to interact. It has sessions on outbreaks, pipelines, bioinformatics tools, antimicrobial resistance, pathogen surveillance and accreditation. This conference attracts public health experts from around the world, including 15 participants from Australia this year including Ben Howden (Director, Microbial Diagnostic Unit, Peter Doherty Institute), Torsten Seemann (also representing Melbourne Bioinformatics), Susan Ballard, Deborah Williamson, Jason Kwong and Sarah Baines from the same group.

Some of the highlights included:

  • A talk by Nuno Faria about the epidemiology of the Zika virus and its transmission from French Polynesia to the USA via Brazil and the Amazon basin. This work was done by driving a combi van around Brazil collecting samples of mosquitoes and sequencing the virus in situ with Minion instruments.
  • Stephen Gillespie from Oxford University gave a presentation on the challenges and benefits to society of the proliferation of semi “real time” sequencing in sepsis and antimicrobial resistance.
  • Paolo di Tommaso gave a talk on a bioinformatics workflow system in an effort to remove hardware differences from workflow outputs.
  • Caroline Colijn gave a very impressive talk on bayesian inference of transmission events and a more robust method for determining them.
  • Eric Marinier, National Microbiology Laboratory, Public Health Agency of Canada introduced their new tool called Neptune.
  • Annamaria Crisan, University of British Columbia, Canada gave an excellent talk about data visualisation.

A number of talks focussed on the proliferation of antimicrobial resistance including an excellent one on carbapenem-resistant organisms in a hospital in Virginia and how they were living in the drains and spreading to various wards etc.

Australia was well-represented. Torsten and I gave e-poster demonstrations of our software (Nullarbor and the GVL respectively), Sarah, Susan and Deborah all gave excellent talks, Jason presented a poster and Ben was a member of the discussion panel on Day 3.

Overall, it was an excellent conference yet again. This was the 4th time I’ve attended this conference with Torsten and others from Australia. Jonathan Green – the conference convener – publicly thanked the international visitors and locals for getting the conference to be more like a movement than a collection of talks. It certainly does feel that way.

Link to conference website.

20-24 May

Microbial Bioinformatics Tools Hackathon

University of Bath – Somerset

Twenty of the conference attendees, from Australia, Portugal, the UK, Sweden and elsewhere, met up at Bath University for a hackathon based around everything discussed at the conference.

I enjoyed teaching a few of the participants how to get their tools into BioConda and as a consequence of this, there are now quite a few microbial-specific tools in BioConda and also BioContainers (automatic from BioConda.) We achieved a lot just in the two days I was there. We also workshopped around the gaps in our tool ecosystem and plans for other tools were drawn up. The hackathon continued for another three days but I had to come back to Cambridge for another one.

22-24 May

Galaxy Training Material Hackathon

Cambridge University Bioinformatics Training Room

This was a joint Elixir/Galaxy Training Network/GOBLET event to expand, compile and collect a lot of the existing Galaxy bioinformatics training material and make it generally available for use and modification.

Participants were from all over the world including Maria Doyle from Melbourne’s Peter MacCallum Cancer Institute. Other attendees included Dave Clements, Mallory Freeburg, Mo Heydrian and Dannon Bakker from the Galaxy project, Björn Grüning, Bérénice Batut, Saskia Hiltemann, Frederick Coppens, Gabriella Rustici, Ralf Weber, Victoria Bohler, Nicola Soranzo and many others from various ELIXIR Nodes and the wider Galaxy community.

The main outcome of the hackathon was a build system and structure for the Galaxy Training Network site and materials. I contributed a number of materials to the site including our Assembly tutorial. We also worked out a way to alter the structure to make it easier for external contributions in future.

The GVL project and Melbourne Bioinformatics has since been invited to assist the ELIXIR Node: France with their 4-day bioinformatics course in early July. The course will be run using the GVL and associated tools.

25 May

EMBL-ABR/ELIXIR-UK Virtual Training Environment Workshop

Cambridge University Genetics Department – Downing Site

This was a workshop led by EMBL-ABR and ELIXIR: UK Node, on the GVL and its implementation in Europe. The participants were Björn Grüning (ELIXIR: German Node), Frederick Coppens (ELIXIR: Belgian Node), Dave Clements and Dannon Bakker (Galaxy project), Yasset Perez-Riverol (EBI and the Biocontainers project), Vicky Schneider (EMBL-ABR and the University of Melbourne), Gabriella Rustici (Cambridge University) and me. I presented the GVL as a cloud bioinformatics platform and solution. We discussed how we could use the GVL along with Galaxy’s CVM-FS and Biocontainers to make bioinformatics tools universally available to biologists and bioinformaticians throughout Europe. We developed a schematic of how we think it will work. EMBL-ABR, Melbourne Bioinformatics and the GVL project now have the opportunity to be a link between parts of the Galaxy project and ELIXIR to help make this a reality.

Several ELIXIR Nodes have expressed interest in getting the GVL working on their clouds so we look forward to closer collaboration with them to help achieve this.

Blog 2…

EMBL-ABR Annual Report 2016

Dear Colleagues

The past twelve months have seen the transformation of this bioinformatics initiative into a structured, networked enterprise. We have demonstrated a working model for maximising the resources and skills existing amongst our own life science community and for mobilising them to connect with international expertise and resources, to ensure our research remains world class.

Our small team at the Hub hosted at VLSCI (now Melbourne Bioinformatics), working with limited resources, has successfully communicated our shared vision and created the mechanisms for the community to come together on our shared objectives.

EMBL-ABR has rapidly garnered significant support and fostered collaborative relationships with the European Bioinformatics Institute, the European Union’s ELIXIR and the United States’ CyVerse and National Institute of Health’s BD2K initiatives, extending the Australian life science community’s national and international engagement activities.

Our thanks to Bioplatforms Australia and the University of Melbourne for their ongoing investment in EMBL-ABR and to all the other people from institutions both here and overseas who have willingly given their own time and energies to us to help us achieve so much to date. It is going to be through that good will that we will be able to demonstrate how a community for bioinformatics can benefit Australian research and industry and thereby attract the necessary infrastructure funding we need to realise our goals.

Finally, our thanks to the team at Melbourne Bioinformatics who rose to the challenge to incorporate these tasks into their already full-time jobs to support so much of the activity as documented in this Report.

We commend this Report to all and thank you for your ongoing interest in, and support for, our work.

Yours sincerely

Assoc Prof Andrew Lonie, Director, EMBL-ABR
Assoc Prof Vicky Schneider, Deputy Director, EMBL-ABR

View and download the Annual Report here.

Limited printed copies have been sent to key stakeholders. Please contact Christina Hall if you would like to receive a printed copy.



Making Sense of Microbial Genomics, UWA workshop November 2016

A 2-day COMBINE workshop was held at UWA over 22/23 November 2016, facilitated by VLSCI’s Simon Gladman and Anna Syme.

This workshop covered Nectar resources, Galaxy, genome assembly and annotation, variant calling and RNA-Seq analysis.

Of the 31 participants, all were very pleased with the whole course:

I thought this was an excellent workshop, I found the information highly relevant and extremely easy to understand – definitely would recommend.
PhD Student, School of Women’s and Infants’ Health, UWA.

The course was excellent even for first time people to use new software.

Great that the ‘why’ of everything was explained – not just the ‘how to'”.


The workshop was part of a series supported by AGTA and VLSCI (now Melbourne Bioinformatics). Full details.

Strengthening our biology backbone – the NCRIS-funded RDS Omics project

Building upon three existing NCRIS-funded capabilities, the Nectar Research Cloud, RDS data services and the Genomics Virtual Laboratory (GVL), RDS Omics empowers the modern biologist to go from raw data to complex, collaborative, downstream analyses without the need to purchase expensive compute or pay for scarce bioinformaticians.

Modern biology is being revolutionised by high-throughput molecular techniques, such as DNA sequencing and other ‘omics’ technologies. RDS Omics is the first Australian platform to allow genomics (DNA), transcriptomics (RNA), proteomics (proteins) and metabolomics (small molecules) data to be efficiently co-analysed, stored, shared and published from one common interface.

What’s been built so far?

A structured data environment, as well as tools and workflows encompassing genomics, transcriptomics, proteomics and metabolomics – and cross-omics systems biology, have now been incorporated into the Platform and deployed on RDS storage and the Nectar Research Cloud.

An online suite of self-directed training materials has already been used in a series of workshops to introduce users to the full capabilities of the platform.

What’s next?

Data from the national Antibiotic Resistant Pathogens Initiative (funded by Bioplatforms Australia) is being uploaded to the Platform through 2017. This will enable timely research on infectious blood pathogens responsible for antibiotic resistant sepsis (blood poisoning). The reference data can then be: co-analysed and stored in one system; managed through a common data management system; have bioinformatics analysis performed on it via a common interface; made accessible to biology researchers in Australia and internationally; and, published to international repositories.

Future releases of the platform are scheduled throughout 2017.

Download news – March 2017 update