First PhD Course a success; bioinformatics survey results; and a new language for a new biology: EMBL Australia in August

13 August, 2013

in Bulletins, EMBL Australia

In this month’s EMBL Australia newsletter:

Posted on  behalf of Professor Nadia Rosenthal of EMBL Australia.

Last month, sixty first and second year PhD students from around Australia came to Melbourne to take part in the inaugural EMBL Australia PhD Course.

Over the two weeks of the course, I watched as these young researchers were inspired by new scientific ideas, connected with other students as well as the speakers, and came into their own as scientists. The speakers, invited from around Australia as well as from EMBL in Europe, also enjoyed the experience and the atmosphere. It felt like I was back at EMBL, with the same excitement and buzz and level of excellence that we strive for there.

One of the students asked me what’s in it for EMBL Australia to hold a course for PhD students. It’s a good question, and one I was happy to answer. Quite simply, we are investing in the future of Australian science, growing future leaders and imbuing them with an international outlook.

When the students heard about the annual EMBL PhD Symposium, which is organised by the first year PhD students at EMBL, I was asked why Australia couldn’t have a conference for PhD students. I’m delighted to announce that the students attending the 2013 PhD course have volunteered to organise their own conference, with the support of EMBL Australia. They plan to invite students from EMBL to attend the conference, just as students from Australia are able to attend the EMBL PhD Symposium through our student grants program.

I’d like to extend my thanks once again to the University of Melbourne, Doug Hilton and the Walter and Eliza Hall Institute for hosting the course, the speakers and the students for your input and enthusiasm, and finally the staff at EMBL Australia, for making the first EMBL Australia PhD Course a resounding success.

Two international visitors will be visiting Australia this month. Mike Hucka will present a series of talks in Melbourne and Sydney about open standards in systems biology research, while Bob Kuhn is bringing the USCS Genome Browser Workshop Roadshow to Brisbane, Sydney, Canberra and Melbourne. They’ll be followed by a series of visits by Japanese science leaders in September and October. More details can be found in the events listings.

Finally, later this month, I’ll be heading off to the 2013 International Conference on Systems Biology (ICSB) with Silvio Tiziani as well as Sarah Boyd from SBI Australia. While there, we’ll be talking about next year’s conference in Melbourne and catching up with some of the scientists working with us to plan the program. I look forward to bringing you more news about the conference in coming months.

First EMBL Australia PhD course a roaring success

Sixty young Australian scientists got a taste of cutting edge life sciences at the inaugural EMBL Australia PhD course last month. The two week program, held at WEHI, offered participants a diversity of life science topics, with a packed schedule of symposium-style presentations and workshops from Australian and international speakers. The PhD Course was modelled on EMBL’s pre-doctoral course, which is compulsory for all of its first year PhD students.

At a reception held for the students and speakers, EMBL Australia’s Scientific Head Nadia Rosenthal welcomed the students to an exciting period in life sciences research. She noted that EMBL Australia existed to foster the creativity of young scientists in Australia and provide a flying start to their careers.

This course feels like EMBL. It has the same exciting vibe and the same level of excellence,” Nadia told students at the PhD Course reception. “This is all about you and all because of you.”

Both students and speakers were enthusiastic about the course.

“The Bioinformatics focus was brilliant, considering the call for molecular biosciences to have those skillsets,” said Laura Baker, a PhD student at the Garvan Institute. “The quality of speakers was fantastic. There was a broad range of topics, something for everyone. It really captured what’s hot in research.”

“We were intrigued with a variety of new questions opening up new corridors of inquiry where we haven’t ventured before,” said Harsha Padmanabhan, from the University of Adelaide. “I experienced the opportunity to go back to ‘class’ and consider why I needed to ask the various questions I was asking through my research, and how to improve my current experiments to get better results.”

Many of the students said hearing from researchers about their own pathways in science was valuable too.

“I really enjoyed being able to hear from such a variety of researchers with so many different stories to tell about their careers. It was really reassuring to hear about all the different ways a research career can unfold,” said Chloe Warren, who is studying at the University of Newcastle.

Students also appreciated the opportunity to meet other young researchers and future colleagues.

“It was great to meet so many other PhD students and to be able to talk about our research and troubleshoot our problems together” said Chloe Warren.

“I now know a lot of motivated young people from a huge range of fields and I am keen to meet them at conferences, share knowledge and collaborate in the future,” said Jasmin Straube, from QFAB at the University of Queensland.

Inspired by their European peers, the students are now organising their own PhD student symposium, which will most likely be held in NSW in late 2014. More details will be available in coming months.

Next year’s course will be held in Perth, Western Australia. Details of the course will be available toward the end of 2013. To register your interest in the course (as a student, as a supervisor of students or as a speaker), please email Jane McCausland: jane.mccausland@monash.edu

BRAEMBL survey results show bioinformatics’ importance to life scientist

Wet lab or dry, Australian life scientists agree that bioinformatics is central to their work, but there’s a real need for better training.

The Bioinformatics Resource Australia-EMBL (BRAEMBL) recently circulated a survey asking Australian researchers to define their bioinformatics requirements. The final report from BRAEMBL’s survey suggests that we could find creative ways to overcome our geographical barriers to share knowledge and bring bioinformatics expertise to more researchers.

The survey, which asked life scientists about their needs and their current usage of bioinformatics resources is now up on the BRAEMBL website. More than 200 responses were received from across Australia, representing 750 researchers from all areas of biology.

Key conclusions were:

  • Bioinformatics is a key activity in Australian research as evidenced not only by the content of responses but also simply by the number of responses
  • The areas of interest reflect the “central dogma” of molecular biology
  • Not only bioinformaticians but also laboratory scientists see bioinformatics as core to their work
  • Geographic location imposes significant but not crippling limitations on exploitation of bioinformatics
  • Users are more likely to report satisfactory service (hardware, software and support) if it is provided within their own group
  • There is a very marked concern about lack of expertise and access to expertise in bioinformatics
  • Training and community building are the most sought after services
  • There is a significant demand for training of a more general nature, in computer programming and statistics

The BRAEMBL team is now working to deliver the bioinformatics capabilities which the survey has identified as most needed by the research community.

Specific areas of action include:

  • Training: BRAEMBL will work with BioPlatforms Australia, CSIRO and other bioinformatics training providers to develop and offer more bioinformatics and statistics training options in Australia.
  • Community building: BRAEMBL will support the role of the Australian Bioinformatics Network in establishing a virtual community for bioinformaticians and other bioinformatics-oriented researchers.
  • User support: Australian users clearly need help in exploiting the tools and data of bioinformatics. The scale and complexity of today’s data resources and services makes it difficult or impossible to copy them all to local systems. While recent IT advances greatly facilitate remote access to tools and services, users are still more comfortable when their bioinformatics needs are satisfied within their own group. A major role of BRAEMBL will be to support users through the inevitable trend to remote access to tools.

Read the full report on the BRAEMBL website.

A new language for a new biology – Mike Hucka on SBML

As one of the developers of the open source Systems Biology Markup Language (SBML), Mike Hucka is an advocate for the benefits of open source collaboration and data sharing.

“Not only do open formats and open-source software allow scientists to share their work even if they use different tools or environments; they make it possible to disseminate, validate and build upon landmark community-oriented efforts, such as the recent model of human metabolism by Thiele et al,” says Mike.

Based at Caltech, Mike is a computer scientist with expertise in a range of fields from artificial intelligence to cognitive science, computer science and computing technologies. In addition to co-developing the Systems Biology Markup Language (SBML) and associated software, he is also a founder of community efforts including COMBINE (the Computational Modelling in Biology Network).

The aim of the project that produced SBML was to write software to support open exchange of models between users and software packages. It has been a great success, with more than 250 software systems across a range of research disciplines now supporting SBML, and it has become a recommended standard for submission of models to many journals such as Nature.

The language can be applied across a broad range of fields from signalling pathway models to neural models, pharmacokinetic models and infectious diseases.

Through this process Mike has become a strong advocate for open source programming and the sharing of scientific data information both across and within research fields. These standards are increasing becoming recommended by some of the world’s leading international journals, so it is important that scientists are up to date with them.

During his visit to Australia he will be discussing an open source approach to science, as well as helping to educate Australian scientists about the benefits of scientific standards.

Meet Mike Hucka in Melbourne and Sydney later this month

Mike Hucka will be visiting both Melbourne and Sydney in August, sharing his experience with open source and how it is helping to foster collaboration.

Join Mike to discuss:

  • How you can use new languages and mechanisms to share your work and collaborate with others here and overseas
  • What role Australia can play in developing computational tools for biology and how we can make an open-source approach work in Melbourne and Australia

Monash Systems Biology Seminar Series: 
Monday 19 August 11am
G29 and G30, Building 82 (New Horizons), Monash University, Clayton Campus. All welcome.

BioMelbourne BioBriefing at St Vincent’s Institute of Medical Research: 
Monday 19 August 4pm
Creating a new language to support open innovation. This event is by invitation only.

Victorian Systems Biology Symposium at the Walter and Eliza Hall Institute:
Tuesday 20 August 11am

A new language for a new biology: how SBML and other tools are transforming computer models of life. RSVP to info@emblaustralia.org

Sydney Computational Biologists Meet-up: 
Wednesday 21 August 5:30pm
Computational approaches to systems biology. Kinghorn Cancer Centre. Details at: www.meetup.com/Sydney-Computational-Biologists/events/133876532

University of Sydney: 
Thursday 22 August 1:30pm
A new language for a new biology; in conversation with Mike Hucka. Places are limited: please RSVP to brooke.white@sydney.edu.au

University of NSW:
Morning tea, by invitation only.

Mike’s visit is supported by SBI Australia with support from the Australian Bioinformatics Network, the Victorian Government, WEHI, The Bio21 Cluster, CSIRO and The University of Sydney.

More details on all of these events at: www.emblaustralia.org/About_us/news/Mike_Hucka

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 close on 12 September 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 modelling of large macromolecular 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.

More details at: http://www.embl.de/training/postdocs/08-eipod/index.html

Events and meetings around the country

UCSC Genome Browser Workshop Roadshow
For 13 years the UCSC Genome Browser has been providing a visual display for genomic data from human and other organisms (now numbering more than 80). Serving nearly 200,000 different users monthly, the browser has grown to be a collection of bioinformatics tools useful for many applications in biomedical research.

In August, Dr Robert Kuhn will be travelling round Australia running a series of workshops on the use and applications of the UCSC Genome Browser. These are open to all researchers, and suitable for all levels of experience from complete novice to experienced user. Workshops will be run in Brisbane, Sydney, Canberra and Melbourne, with an Introductory seminar and an advanced hands-on workshop session to be held in each city.

The UCSC roadshow is organised by QFAB and supported by the Australian Bioinformatics Network, in partnership with the Institute for Molecular Bioscience, VLSCI, the Garvan Institute, CSIRO and the Genome Virtual Laboratory.

For information on dates and contacts please visit http://www.qfab.org/event/ucsc-genome-browser-roadshow/

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

August
15 to 23 August – UCSC Genome Browser Roadshow, Brisbane, Sydney, Canberra, Melbourne
19 August – BioMelbourne BioBriefing: Creating a new language to support open innovation, St Vincent’s Institute, Melbourne
20 August – A new language for a new biology: How SBML and other tools are transforming computer models of life, Walter and Eliza Hall Institute, Melbourne 21 August – Computational Approaches to Systems Biology, Kinghorn Cancer Centre, Sydney
29 August to 4 September – 2013 International Conference on Systems Biology, Copenhagen

September
29 September to 3 October – ComBio 2013, Perth

November

21 to 23 November – 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: www.emblaustralia.org

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