EMBL-ABR 2016 Annual Report now online

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EMBL-ABR 2016 Annual Report now online

Category : news

May 2017


The 2016 EMBL-ABR Annual Report, documenting our key achievements in 2016, is now available ONLINE.

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 investment in bioinformatics infrastructure can benefit Australian research and industry and thereby attract the necessary 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 you, and thank you for your ongoing interest in, and support for, our work.

Yours sincerely

Assoc Prof Andrew Lonie, Director                       

Assoc Prof Vicky Schneider, Deputy Director, EMBL-ABR


Hard copies are being sent out to key stakeholders, please contact Christina Hall if you would like to receive one.

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EMBL-ABR network: an interview with Rochelle Tractenberg

Director, Collaborative for Research on Outcomes and -Metrics, an institute she established, Rochelle Tractenberg is a multi-disciplinary expert who brings many years of experience as a statistician to her insights into the fast-moving world of bioinformatics. She has a great deal to say about Open Science in this month’s interview, and concludes:

There are international efforts in bioinformatics and in open science (and in open bioinformatics science), and describing, committing to, and sharing an Australian model that prioritises rigour, reproducibility, engagement and transparency could exert a positive influence on these international conversations.

Full interview.

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EMBL-ABR: an interview with Lavinia Gordon

Category : Uncategorised

Lavinia Gordon has been a practising bioinformatician for many years now and has a clear grasp of the daily issues confronting life science researchers in analysing and managing their data, issues which have been changing as the field matures. We asked her specifically how she saw a national, federated bioinformatics infrastructure would benefit AGRF and her response was immediate: “we have a large client base who are open to sharing and collaborating so an infrastructure that is easy for them to access and is appropriately resourced would be massively beneficial”. It is for this reason that AGRF has come on board as an EMBL-ABR Node.

Full story.

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EMBL-ABR network: an interview with Dieter Bulach

Category : Uncategorised

Dieter Bulach is well known in the microbial genomics community and works at both the VLSCI and the Peter Doherty Institute in Melbourne, Australia, on a range of important public health projects. He has just been appointed as the EMBL-ABR Activity Lead for Prokaryotes Bioinformatics. In this interview, Dieter identifies the growing role for bioinformaticians as not only collaborating with researchers to analyse data, but to lead the evolution of standards and systems to maximise the accessibility of the data once it has been published, for the wider research community. That just about sums up what EMBL-ABR is trying to achieve and why he has taken on this role.

Full story.

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New Galaxy Australia community opens registrations for GAMe 2017

Category : Uncategorised

3 October 2016

Today we officially launch the Galaxy Australia community with the opening of registrations for the Galaxy Australasia Meeting 2017 (GAMe 2017) being held in Melbourne over 3-9 February. Australian Galaxy users and administrators will now have more opportunities to interact and collaborate to identify and address the needs of the local community. The community will also be a hub for Australian Galaxy training courses and offer a catalog of Australian Galaxy servers.

The establishment of Galaxy Australia is supported by the EMBL Australia Bioinformatics Resource (EMBL-ABR) in its appointed role of supporting the development of skills and training in the Australian life science research community. At the EMBL-ABR Hub, hosted at the Victorian Life Sciences Computation Initiative (VLSCI), Galaxy is used extensively for teaching and data analysis directly as well as through the Australian-made Genomics Virtual Laboratory. VLSCI’s expert bioinformaticians and professional staff will help promote community activities and training.

Galaxy Australasia Meeting 2017 (GAMe 2017)

The Community’s first major activity is to organise the Galaxy Australasia Meeting 2017 (GAMe 2017), 3-9 February in Melbourne.

We are pleased to announce that early registration and talk and poster abstract submission are now open for the GAMe 2017. This meeting will bring together biomedical researchers, bioinformaticians, infrastructure providers, and data producers from across Australia and Asia to share expertise across many levels.

The conference starts 4 February and features two full days of keynotes, accepted and sponsor talks, poster and sponsor sessions, birds­-of-­a­-feather gatherings, a conference dinner and lots of opportunities for networking.
Prior to the conference we are offering a Researcher Training Day on 3 February, aimed at biomedical researchers who need to analyse their biological data.

The conference is followed by a four day workshop on Galaxy server administration for those working at that level.

Talk abstracts are due 30 November and early registration ends 31 December.

Register now and save up to 43% off regular registration rates.

There are also scholarships available for eligible students and postdocs. The scholarship application deadline is 18 November.

We look forward to welcoming you to Melbourne. Remember to pack for our fabulous February weather!

GAMe 2017 Organising Committee (#game_2017)

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EMBL-ABR network: an interview with Rudi Appels

Category : Uncategorised

The International Wheat Genome Sequencing Consortium (IWGSC) is a collaborative project doing for agriculture what the human genome sequencing project is delivering for medicine: a “gold standard reference sequence” or the complete map of the entire genome. The aim is to precisely position all genes and other genomic structures along the 21 wheat chromosomes. It is a big job, with the wheat genome being five times larger than the human genome.

Australian researchers are playing their part. Murdoch University Professor Rudi Appels is one of six co-Chairs of IWGSC and his team is working on sequencing chromosome 7A, one of 21 chromosomes in wheat. Prof Appels says this will eventually lead to “improved wheat varieties with important agricultural traits such as yield increase, stress response, and disease resistance, as well as having access to diagnostics for diagnosing unexpected problems that come up.”

The big task now is, how do we fulfil our obligation to international collaborators to share this data with researchers around the world? What infrastructure and skills are needed to be in place before farmers reap these benefits? This week we asked Professor Appels.

Full story.

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EMBL-ABR network: an interview with Sandra Orchard

Category : Uncategorised

Deputy Director Vicky Schneider caught up with EBI’s Sandra Orchard while visiting EBI over August. She took the opportunity to interview Sandra for our ongoing series. When asked about Open Data, Sandra threw out the challenge to us all: “placing raw data onto GitHub or FigShare or even on a poorly advertised, local website may appear to tick the Open Data box, but in reality falls well short of community needs.”

Sandra is one of the international faculty joining us for the Best practice workshop series: the Data Life Cycle being held in Melbourne in October.

Full story.

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Australia now Biosharing through agreement finalised this week

Category : Uncategorised

From this week Australian researchers are able to contribute their materials to this portal and to get access to its store, thanks to an agreement between Biosharing and EMBL-ABR. Such access will enable further dissemination of shared data standards for researchers around the world.

Biosharing is a web-based, searchable portal of three interlinked registries, containing both in-house and crowd-sourced, manually curated descriptions of standards, databases and data policies, combined with views, collections and recommendations across all three registries.

Australian Bioinformatics is growing in capacity and influence and Australian bioinformaticians can leverage Biosharing to not only see what is already available, but to highlight their databases and standards to an international audience and link them into the BioSharing ecosystem, providing context and increased visibility for those resources.

This week we caught up with Dr Peter McQuilton, Knowledge Engineer/Senior Research Associate and content lead for the BioSharing project led out of the University of Oxford’s e-Research Centre, to get a better understanding of what BioSharing is all about.

Full details.

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EMBL-ABR: an interview with Jenny Martin

Category : Uncategorised

This week’s interview is with high-achieving Professor Jenny Martin, Director, Eskitis Institute, Griffith University in Australia. We are extremely pleased to announce that Jenny has agreed to join our International Science Advisory Group. 

Jenny’s comments on data and publishing models confirm some strong themes coming through from the research community in these interviews. We welcome what we know will be her robust contribution and guidance for our growing network.

Read more.