Copy
View this email in your browser
EMBL Australia, learning, growing, networking
Dear Sir/Madam

This month I would like to draw everyone’s attention to the amazing infrastructure readily accessible to all Australia scientists as a result of Australia’s Associate Membership of the EMBL. By infrastructure, I mean people and facilities.  Here at EMBL Australia we have many leading scientists in world class facilities that are easily accessed.  Some of this information in now available in our annual report – please take the time to take a look!

I encourage Australian life science researchers to seek them out and question how they can make meaningful connections and apply the expertise available to further their own research. One such piece of amazing infrastructure that I am highlighting this month is the EMBL Australia Bioinformatics Resource (BRAEMBL) as it coincides with an important visit from Dr Nikolas Blomberg - a world leader in bioinformatics from ELIXIR  (see article below). 

In this regard it is also great to see our students are leading by example.  Australian students that recently attended EMBL PhD Student Symposium in Heidelberg are embracing collaborating opportunities abroad and using this opportunity to develop relationships at EMBL and exploring new research techniques. (For full report on students see article below.)

On a personal note, I just wanted to publicly thank my colleagues at the Australian Academy of Health and Medical Sciences in nominating and electing me as a fellow of this prestigious organisation. It is very humbling to be recognised for “distinguished professional achievement and outstanding leadership’ by such a successful group of leading scientists. 

Nadia
 
Professor Nadia Rosenthal
Scientific Head, EMBL Australia

Please note that all replies to this newsletter go to info@emblaustralia.org. If you wish to email me directly, my address is nadia.rosenthal@emblaustralia.org.

In this month's newsletter:

Remarkable research infrastructure that can be accessed at EMBL Australia - BRAEMBL


The EMBL Australia Bioinformatics Resource is one of the incredible research infrastructures established with the support of EMBL Australia and Australia’s Associate membership of the EMBL.

The EMBL Australia Bioinformatics Resource (BRAEMBL) now links Australian researchers with access to the Victorian Life Sciences Computation Initiative (VLSCI) high-end systems along with over 240 software programs used in life sciences research, technical experts and bioinformatics training and expertise. Established with the support of EMBL Australia and Australia’s Associate membership of the EMBL, BRAEMBL is now evolving to address the changing needs for bioinformatics expertise in Australia.
 

New Host Institution 


From 2015, through an agreement between Bioplatforms Australia and the University of Melbourne, relocation of the BRAEMBL to VLSCI is focusing the next phase on addressing the increasing demand for training and skills development in bioinformatics while concurrently continuing to develop tools and resources for the Australian research community and our international collaborators. With the successful roll out of the Australian-made NeCTAR-funded Genomics Virtual Laboratory (GVL), with training materials developed by VLSCI bioinformaticians, much of the training to be delivered will be offered on this platform.

The new agreement involves a network of service providers at nodes in Queensland (QCIF), New South Wales, (The University of Sydney Schools of Biological Sciences and Medicine), Western Australia (Centre of Excellence in Plant Biology), Adelaide, (University of Adelaide, Flinders University and SAHMRI) and Tasmania (Menzies Research Institute), making it truly national. The nodes will provide local training and researcher support, plus bioinformatics tools and platform access, modelled on the successful services delivered at VLSCI over the past five years. 

In an acknowledgment of this success, Assoc Prof Andrew Lonie, appointed Director, BRAEMBL in early 2015, was recently appointed as Director, VLSCI.
 

Workshops


Local and national workshops are being rolled out across Australia. Some are being run by Bioplatforms Australia and CSIRO and some are being run by VLSCI bioinformaticians. If your institution would like to host a workshop, or set up an instance of the GVL through which to do research or deliver training, please contact the VLSCI/BRAEMBL Communications Team through Helen Gardiner at hg@unimelb.edu.au or Dr Christina Hall at crhall@unimelb.edu.au, Communications Officer.
 

Websites


The Resource is still located at www.ebi.edu.au (redirecting also from www.braembl.org.au), and is now hosted at VLSCI. If there is some lost functionality that you are experiencing, please submit your problem via the help desk on the website. Data hosted at www.ebi.edu.au is currently still hosted on that server located at the University of Queensland (UQ).
 

Data Resources & Tools - updates

  • Ensembl Genome Browser. This now redirects to http://asia.ensembl.org.
  • Australian Species Data remains as is.
  • Meme-suite. Co-developed at UQ, this tool is no longer being maintained on ebi.edu.au and is now located on the cloud at meme-suite.org. Any queries about its functionality or uses can still be sent to meme-suite@uw.edu
  • GT-Scan. Developed in Australia and maintained by Aidan O’Brien at CSIRO, this is in the process of being transferred over to VLSCI systems but still runs from its original site. Any queries about GT-Scan can be sent to gt.scan.comtact@gmail.com.
  • NCI-SF. The NCI-SF facility is now closed. Get advice from VLSCI experts on the best place to run your bioinformatics. 

Feel free to contact Assoc Prof Andrew Lonie, Director, EMBL Australia Bioinformatics Resource, anytime via alonie@unimelb.edu.au or 03 8344 1395, 0406 487 902.

The EMBL, University of Melbourne and VLSCI's logos

Dr Niklas Blomberg, Director, ELIXIR, EMBL (UK), visiting in early December


ELIXIR is an international response to the problem of ‘big data’ and it has a key role to play in linking global data resources. Dr Blomberg will be seeking out collaborations and discussing common methodologies. 

Located within the EMBL-EBI building in the UK, Dr Blomberg's team has responsibility for coordinating this pan-European distributed research infrastructure for the sharing of life science data – a problem all involved in this field are focused on trying to address. 

Engagement with ELIXIR adds a vital link to existing EMBL relationships and our bioinformaticians and research infrastructure policy leads are looking forward to seeing how to Australian researchers can work with ELIXIR to maximise connections to this important enterprise.

Headshot of Nikolas BlombergStarting in Melbourne (30 Nov), Dr Blomberg will meet with BRAEMBL node heads and senior bioinformatics leads, as well as the broader life sciences computing community in some round table discussions on global trends in bioinformatics and big data. From there he will head to Brisbane (1 Dec) for meetings before being involved another round table in Canberra (2 Dec) with representatives from academia, government, research infrastructure funding agencies and other guests keen to hear about ELIXIR and how Australian researchers might be involved. The tour end will end in Sydney (3 Dec) with another series of meetings.

Also joining the roundtable in Canberra is computational biologist, Dr Vivien Bonazzi, Senior Advisor for Data Science Technologies at the US National Institutes of Health. This presents a wonderful opportunity to share experiences and reflections across both the EU and the USA. 

Thanks Andrew for all the hard work you have put in to making this important event happen.

To participate in the program, email Helen Gardiner - hg@unimelb.edu.au or visit the website http://www.ebi.edu.au/news/elixir. To discuss BRAEMBL/ELIXIR plans, please contact Assoc Prof Andrew Lonie - alonie@unimelb.edu.au or 03 8344 1395. 

Dr Max Cryle appointed as EMBL Australia, Group Leader, Monash University


Dr Max Cryle is originally from Australia where he trained as an organic chemist at the University of Headshot of Max CryleQueensland.  Following his PhD, Max made the bold move to the Max-Planck Institute for Medical Research (MPIMF), in Heidelberg, Germany. Max is currently an Emma-Noether Independent Group Leader at the MPIMF, where he established a group to further understand the later crucial stages of glycopeptide antibiotic biosynthesis. Max’s research is based at the interface of chemistry and biology using a combination of chemical synthesis, biochemical characterisation and X-ray crystallography. 

Congratulations Max and welcome to the EMBL Australia family.

Profile - Prof Thomas Preiss, EMBL-Australia, Collaborating Group Leader, ANU


Thomas originally started his academic career in Germany where he studied Chemistry at the Philipps-Universität, Marburg and the University of Bristol (UK) from 1986-91. He then chose to stay in the UK to undertake his PhD at the University of Newcastle upon Tyne (UK) (1992-95). Thomas then spent 7 years (1995-2002) as a postdoctoral scientist at EMBL, Heidelberg (Germany).

In 2002, he moved to Australia as a laboratory head at the Victor Chang Cardiac Research Institute in Sydney and held conjoint appointments at the University of New South Wales (Senior Lecturer, then Associate Professor). In 2011, he moved to the ANU and accepted a position as Professor of RNA Biology at ANU/JCSMR.

Headshot of Prof Thomas PriessProfessor Preiss is a molecular biologist determining the mechanisms and transcriptome-wide patterns of eukaryotic mRNA translation as one of life’s core processes and its regulation by RNA-binding proteins and non-coding RNA as a means of controlling gene activity. Since joining the translational control field in 1995 as a postdoctoral scientist, he has since had a particular focus on mechanisms of translation initiation using yeast and mammalian cells and cell-free translation systems as his preferred models. He also studies global patterns of post-transcriptional control using microarray and next gen sequencing-based methods. After starting his own group he continued to investigate the role of the mRNA cap and poly(A) tail and associated protein factors in determining mRNA utilisation. These studies overlap with work on the discovery of miRNA targets and the unravelling of their mechanism of action. Employing next gen sequencing technology (RNAseq), his group is further pursuing interests in the area of RNA (mRNA, miRNA, tRNA, other noncoding RNA) processing, modification, polyadenylation and utilisation.

As an EMBL alumni, Thomas is a very strong advocate of EMBL Australia. He still collaborates directly with EMBL Europe and many here at EMBL Australia. 

You can contact Thomas on: E: thomas.preiss@anu.edu.au; T: +61 2 6125 9690
 
EMBL Australia is keen to acknowledge other Australian researchers having active collaborations with EMBL scientists. An EMBL - Australia Collaborating Laboratory is defined as an active collaboration between a research group in Australia and an EMBL group that: 
  • has shared funding/grant applications
  • has shared bylines on publications
  • is, or is expected to be longstanding (min 2 years), and
  • necessitates geographical exchange of staff and students as appropriate.
If you or a scientist colleague has such a collaboration and would like to be more involved in EMBL Australia activities as a collaborating group leader please contact Silvio Tiziani, Executive Director, EMBL Australia at silvio.tiziani@emblaustralia.org.au or on (03) 9902 9603.

Feedback from Student PhD Symposium and EMBL Noncoding Genome Conference, EMBL Heidelberg


As reported previously, there were ten postgraduate students that were awarded travel grants to travel to EMBL-Heidelberg recently to attend the annual EMBL student symposium and EMBL Noncoding Genome conference. The symposium proved to be an excellent growth opportunity for our students and one where they were given a chance to develop their international networks and alliances and ‘calibrate’ their work via EMBL’s programs. For most of these students it was their first international symposium and first time presenting at an international conference. Some of the student’s comments were:

“I have gained so much more than I expected – I can see so many opportunities available at EMBL. I met my research peers around the world, had high level discussions with the leaders in my research area and viewed the facilities at EMBL Heidelberg. Most importantly, listening to some of the presenters talk about the techniques used in my area of science - I will now pursue these in future experiments. I also learned about science communication and scientific publishing which has given me an appreciation for aspects of science seldom discussed at other conferences, and will be invaluable in my scientific career.”

‘I received a range of valuable feedback on my current project – including suggestions of several ideas/analysis that I had overlooked and will be following-up on. I have made contacts with other researchers in my field, one particular contact that is very interested in my work. We are in ongoing correspondence, looking to develop a collaboration between our groups.”

“The two symposiums were a great experience and certainly were a benefit to my ongoing development as a scientist” 

Congratulations to all the students on their presentations.

EMBL Heidelberg - seeking highly motivated student to join the Protein Expression and Purification Core Facility


EMBL Heidelberg is looking for a motivated student to experiment with several protein expression and purification methods for different Cas9 variants (e.g. wild type, nickase and deadCas9). After development of a suitable in vitro activity assay, the purified Cas9 proteins will be implemented in vivo in various scientifically relevant cellular systems. 

This project will provide the opportunity to gain in-depth knowledge of modern recombinant protein expression and purification methods as well as gaining experience with cell biology techniques in the frame of the scientifically hot topic CRISPR-Cas9. 

For more information or applications, please contact Dr Kim Remans by sending an e-mail to pepcore@embl.de.

Reminder, BioInfoSummer – 2015, University of Sydney

7-10 December, 2015


There is still time to catch up on the latest bioinformatics techniques and approaches if you register now. BioInfoSummer provides bioinformatics training to students, researchers and others working in related areas and is fantastic fast-track program that is full of information and opportunity. National and International speakers will be speaking at this year’s BioInfoSummer. To see who is speaking visit www.bis15.amsi.org.au. Speakers are listed as they are confirmed so check the website for regular updates.

This year, the BioInfoSummer event will include both specialist lectures and hands on introductory and advanced computer workshops. The topics being discussed this year include:
  • Introduction to Biology and Bioinformatics
  • Epigenomics
  • Translational Genomics
  • Proteomics and Metabolomics
  • Systems Biology, Networks and Data Integration

Poster abstract submissions closes: 6 November, 2015

Registration closes: 27 November, 2015

If you are a students living outside of Sydney you could be eligible for up to $500 in travel support being offered by The Australian Bioinformatics Network, EMBL Australia, Bioplatforms Australia and CSIRO. Travel grants are now open.

Join the conversation on Facebook and Twitter.

BioInfoSummer Logo

Internships still available for MSc or PhD students at Merrimack Pharmaceuticals 


Merrimack Pharmaceuticals is offering a variety of internships, which are open to EMBL Australia students/staff. Further information can be found on the EMBL website.

If you are interested in joining the Merrimack internship program contact interns@merrimackpharma.com

About EMBL Australia


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 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
Twitter
Twitter
Website
Website
LinkedIn
LinkedIn
Copyright © 2015 EMBL Australia, All rights reserved.


unsubscribe from this list    update subscription preferences 

Email Marketing Powered by Mailchimp