Building links between sciences; international training for bioinformaticians; and launching our PhD Course

Bulletins, EMBL Australia

In this month’s EMBL Australia newsletter:

Posted on  behalf of Professor Nadia Rosenthal of EMBL Australia.

This week, we welcome 60 bright young scientists to Melbourne for the first EMBL Australia PhD Course.

These PhD students have come from around Australia to spend two weeks immersed in the latest ideas, techniques and new technologies in life science.

Our aim is to give these students, who are just embarking on a career in research, a taste of scientific diversity, some useful tools and ideas for their projects and perhaps most importantly, a network of scientific contacts across the country.

I’m proud to be able to offer this course in Australia for the first time. It’s based on the annual training course which entering PhD students at EMBL complete before starting their research at EMBL’s labs across Europe.

I’ve seen first-hand how valuable the early immersion course could be for my students at the Rome-Monterotondo Outstation: they came back to the bench armed with knowledge of the latest concepts and techniques being used across EMBL. And through their networking over the course of ten weeks, they knew exactly who amongst EMBL research groups and fellow students to contact for more information or support when they needed it for their own work.

The course is just one of our initiatives to support young scientists. Australia’s associate membership also allows us to send 20 Australian students to join the annual EMBL PhD Symposium, and we’re offering student travel grants of up to $3500 to attend this exciting event every year.

There’s also a unique opportunity for post-doctoral students to pursue multidisciplinary research with three years of funding from the EMBL Interdisciplinary Postdoc program. The EIPOD program specifically recruits early-career scientists to find synergies at the borders of related fields of science, and to apply techniques in new contexts.

Finally, I’d like to highlight a training program offered by our colleagues at Bioplatforms Australia and CSIRO. The Next Generation Sequencing Workshop, which originated at the EMBL European Bioinformatics Institute, has been tailored to give Australian life scientists hands-on experience in genomic sequence analysis.

It’s already been a great success, bringing new bioinformatics expertise into Australia, building our bioinformatics capabilities by offering these tools to scientists who need them across the country. Rotating workshops have been held in Sydney, Brisbane, Adelaide and Perth, and will be in Melbourne next week.

EMBL Australia PhD course kicks off in Melbourne this week

This week, 60 of Australia’s best young PhD life science students are coming to Melbourne for EMBL Australia’s first PhD Course.

In the next two weeks, we’ll give them a taste of the latest developments in life science, from structural biology to animal models, developmental genetics to next gen sequencing, biomedical imaging to science communication.

Faculty are flying in from EMBL in Europe and from across the country to contribute to this important event in the development of EMBL Australia, as we work to capitalise on Australia’s membership of the European Molecular Biology Laboratory.

The course is based on a program from EMBL – the European Molecular Biology Laboratory. Their first year PhD students start their training together with an immersion course in the full range of life science research. There’s an emphasis on developing a curiosity for new ideas and a collaborative spirit.

Our first cohort of 60 first and second year PhD students will spend two weeks at The Walter and Eliza Hall Institute for Medical Research (WEHI) with lectures and workshops from top Australian researchers, including WEHI bioinformatician Terry Speed, ANU molecular biologist Thomas Preiss and UNSW systems biologist Marc Wilkins.

We’re also welcoming Matthias Wilmanns, Vladimir Benes, George Papadatos and Marcus Heisler to join our teaching faculty from the European Molecular Biology Laboratory.

The students have come from all over Australia to join the program:

  • New South Wales, 18 students: University of Sydney, University of NSW, University of Newcastle, Macquarie University, The Garvan Institute, ANZAC Research Institute, Brien Holden Vision Institute
  • South Australia, 6 students: University of Adelaide, University of South Australia, Flinders University
  • Queensland, 7 students: University of Queensland (inc IMB, QFAB), Griffith University, CSIRO
  • Victoria, 19 students: Monash University (inc ARMI), University of Melbourne, La Trobe University, Peter MacCallum Centre, University of Ballarat, Murdoch Children’s Research Institute, St Vincent’s Institute
  • Western Australia, 4 students: University of Western Australia, Curtin University, Telethon Institute
  • Australian Capital Territory, 6 students: Australian National University (inc John Curtin School of Medical Research)

Simone Li: welcoming Australian students to EMBL

This year’s 15th EMBL PhD Symposium has a unique Australian angle – one of the first year PhD students organising the conference is Simone Li, who is at EMBL through the EMBL Australia International PhD Program.

The PhD Symposium is organised each year by first-year PhD students at EMBL, and includes networking opportunities, poster sessions and workshops with experts. It brings together fellow students from around the world for a three-day series of talks by leading experts but also by students themselves. It’s an opportunity to make connections with students from around the world and get new insight into your own research direction.

“I am excited to be co-ordinating the EMBL International PhD Symposium this year. It is a conference fully organised by the first-year PhD students – we actually come up with the theme and program, and have to find funding!” Simone says. “And I’m looking forward to meeting this year’s cohort of Australian students and showing them around EMBL too!”

And Australian PhD students are invited to apply for one of 20 travel grants to attend the PhD Symposium in Heidelberg, Germany.

Apply online for one of 20 travel grants to attend the symposium at:

NGS Workshops: a great model for advanced international training

Over the last 12 months more than 140 researchers have attended Next Generation Sequencing workshops around Australia.

The workshops, run by Bioplatforms Australia and CSIRO, introduce bench scientists with little knowledge of bioinformatics to the basics of next generation sequencing data analysis, including Illumina next generation sequencing data quality, sequence alignment algorithms, ChIP-Seq analysis, RNA-Seq analysis, de novo genome assembly and an introduction to the command line interface.

Bioplatforms Australia chief Andrew Gilbert says the workshops grew out of the recognition that there were just not enough bioinformaticians available in Australia to perform sequence data analysis for all potential users.

“We saw a massive shortfall in hands-on skills, and an opportunity to train regular bench biologists to do their own analysis,” Andrew says. “Initially we brought out trainers from EMBL-EBI to do a workshop, but it was clear to us that the best way forward was to send a delegation of our own bioinformaticians to the UK to train as trainers, so we could run our own workshops tailored to local needs.”

He notes that the benefits to workshop participants are not restricted to the skills learned in the workshops.

“The scientists who do the workshop come away with a permanent connection to a network of bioinformaticians, a resource for the future,” Andrew says.

The NGS trainers have now run workshops in Melbourne, Sydney, Brisbane, Adelaide and Perth. Another delegation of trainers will be travelling to the UK later this year to refresh and update their skills.

It’s also a model that Andrew Gilbert believes could be successfully used to teach other bioinformatics and life science skills and technologies to bench scientists.

“We expect that ultimately, the Australian Bioinformatics Network will provide similar courses to the Australian life science community,” says Andrew.

“Pick a gene and get started”: Howard Jacob on the future of personalised medicine

Howard Jacob is a pioneer of ‘personalized medicine’: a couple of years ago, he and his colleagues successfully treated a five year old with a life threatening digestive condition by sequencing the boy’s genome to find a rare mutation.

howard news 24

With his genome on his iPad, Howard Jacob told ABC News Breakfast about the possibilities of personalised medicine

It’s a controversial idea, especially in the US, but now that we can sequence a whole human genome for a few thousand dollars (as opposed to a few billion dollars), it’s feasible.

He spoke this month with doctors and researchers at the Royal Children’s Hospital in Melbourne, telling the crowd at the first Victorian Systems Biology Symposium that they should explore the potential of whole genome sequencing even though we don’t yet have all the answers.

Prof Kathryn North, director of the Murdoch Childrens Research Institute, said at the symposium that even in cases where a cure isn’t available, genome sequencing can give parents the peace of mind of a firm diagnosis.

“Genome sequencing is the first step towards developing therapies for rare genetic diseases. We don’t yet have all the answers, but that shouldn’t hold us back,” says Kathryn. For the parents of the very sick children we see at the Royal Children’s Hospital and the Murdoch Children’s Research Institute, a diagnosis can be life-changing.”

Howard is planning a $60 million genomics centre at the Medical College of Wisconsin, which recently became the first in the world to offer complete whole genome sequencing (WGS), from patient consent through the return of clinical results, to patients worldwide.

While in Melbourne, he also chatted with research and health leaders. And you might have caught him on ABC 24 News Breakfast, or spotted him in The Age and Sydney Morning Herald.

Building links between sciences: interdisciplinary post-docs wanted at EMBL

Create new connections or move into a new field of research with a three year postdoc interdisciplinary fellowship at EMBL.

Applications are open now for the EMBL Interdisciplinary Postdoc program, which specifically recruits early-career scientists to find synergies at the borders of related fields of science, and to apply techniques in new contexts.

Projects funded in the 2012 EIPOD program included:

  • In vivo analysis of mRNA trafficking
  • The role of cellular proteins in HIV budding
  • Engineering and visualization of chromatin loops
  • Integrative modeling of large marcromolecular assemblies

Candidates are invited to propose and design an interdisciplinary project of their choice, which should involve at least two EMBL groups from any of the five EMBL sites in France, Germany, Italy or the UK. Or you might choose to develop an existing project.

Fellows come from a wide range of backgrounds including, biology, chemistry, biochemistry, molecular biology, medicine, engineering, physics, mathematics, computer science and bioinformatics.

The EIPOD program is open to all nationalities and Fellows come from a wide range of research backgrounds. Its only criteria are scientific excellence and interdisciplinarity.

About 20 positions are available. Applications for 2013 open on 1 July and close on 12 September.

More details at:

Events and meetings around the country

Next Generation Sequencing Hands-on Workshop in Melbourne

Monash University, 10-12 July, 2013

This is a practical three day hands-on course is designed for bench biologists, PhD students or early career postdoctoral researchers with no or basic bioinformatics experience who are planning or currently using NGS approaches in their research area. It will include a half-day introduction to the command line interface.

This course is designed to familiarise participants with next Generation Sequence data analysis and to provide hands-on computational experience in analysis of NGS data using common analytical approaches for ChIP-seq, RNA-Seq data and de novo genome assembly.

Registration has closed but for more information on the program contact: Catherine Shang, or Annette Mcgrath

Read more of the program at:

The course is one of a series around Australia, based on a program from the EMBL-EBI in Hixton, UK, offered jointly by Bioplatforms Australia, CSIRO and EMBL Australia.

Upcoming events and deadlines

If you have events to add to the EMBL Australia events calendar, drop us a note on with the details and a link for more information.


30 June to 12 July – EMBL Australia PhD School, Melbourne

1 to 5 July – Winter School in Mathematical and Computational Biology, University of Queensland

10 to 12 July – Next Generation Sequencing Hands-On Workshop, Monash University, Melbourne 

19 July – Applications close for the EMBL Australia PhD travel grants


19 August to 23 August – Mike Hucka – Melbourne

29 August to 4 September –  International Systems Biology Conference, Copenhagen


29 Sept – 3 Oct – ComBio 2013, Perth

30 Sept to 4 Oct – Practical Workshop on High-Throughput Sequencing Data Analysis, OIST, Okinawa, Japan


21 to 23 Nov – EMBL PhD Symposium, Competition in Biology: The Race for Survival from Molecules to Systems, Heidelberg, Germany

Australia’s membership of EMBL

EMBL – the European Molecular Biology Laboratory – is Europe’s flagship for the life sciences. The Australian government joined EMBL as an Associate Member in 2008.

EMBL Australia was created to maximise the benefits of Australia’s associate membership of EMBL. It creates opportunities for:

  • internationalising Australian research
  • empowering and training our best early career researchers/research leaders
  • embedding powerful new enabling tools such as bioinformatics and systems biology in Australian life science.

EMBL Australia comprises:

  • Victorian node at Monash University, with two research groups and SBI Australia (Systems Biology Institute)
  • South Australian node at SAHMRI, opening in 2013 with three research groups
  • Queensland node at the University of Queensland with the Bioinformatics Resource Australia and plans for future research groups
  • NSW node at the University of Sydney with one research group (currently based in Europe) and plans for future research groups
  • Australian Bioinformatics Network, based at CSIRO
  • A node will be developed at the University of Western Australia as funds and opportunities arise.

EMBL Australia is an unincorporated joint venture between members of the Group of Eight universities and the CSIRO, supported by the Australian government.

Read more about EMBL Australia at:

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