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Bioinformatics expertise shared across Australian network assists international research collaboration

When listening to the needs of research groups around Australia, we hear that bioinformatics challenges come in all shapes and sizes. Sometimes very specific skills are required to solve particular problems sporadically throughout a project, and often the required expertise can’t be found close at hand. The benefits of an informed network that shares knowledge

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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

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Open Science: an interview with David Lynn

This month we are pleased to interview Assoc Prof David Lynn. Since 2014 David has been a European Molecular Biology Laboratory (EMBL) Australia Group Leader at the South Australian Health and Medical Research Institute (SAHMRI). He is also an Associate Professor at Flinders University School of Medicine. His group has built up considerable resources for

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Best Practice Data Life Cycle Approaches for the Life Sciences, now on F1000Research

Following our very successful data life cycle workshops held in Melbourne in October 2016, the feedback, findings and further reflections are now published online at bioRxiv: http://www.biorxiv.org/content/early/2017/07/24/167619. The paper has since been accepted for publication at F1000Research and open to peer review. From the Abstract: Throughout history, the life sciences have been revolutionised by technological advances; in

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Open Science: an interview with Graham King

Today we are very pleased to be publishing our next Open Science interview conducted with Prof Graham King from Southern Cross University, head of our 12th EMBL-ABR Node. Graham’s interest in Open Science is in its potential for Australian scientists to showcase their science and draw attention to the knowledge generated here, especially in fields

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Open Science: an interview with Saravanan Dayalan

Saravanan Dayalan is passionate about Open Science. He encourages young life science researchers to investigate how to expose and maximise their research to benefit their careers. And to the community overall, he says we need to learn from and adopt methods from the physicists, who have been successfully doing open science for decades now. Full

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Open Science: an interview with Jeff Christiansen

This month we are very pleased to publish an interview with Jeff Christiansen, Health and Life Sciences Program Manager, QCIF.  In early August Jeff will be taking over the role of Open Data Coordinator, EMBL-ABR whilst Pip Griffin takes some family leave. Jeff has loads of experience in the area of open data and some thoughtful

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EMBL-ABR 2016 Annual Report now online

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May 2017 A LETTER FROM THE DIRECTORATE 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

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Open Science: an interview with Rob Lanfear

ANU Senior Researcher Rob Lanfear left evo-devo research for the more open community engaged in bioinformatics. He loves the fast-paced action in his field, which he feels must be kept open if it is to deliver timely research outcomes: Nanopore sequencing is the best example I can think of. This is an exceptionally fast-moving field,

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EMBL-ABR network: an interview with Rochelle Tractenberg

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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

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EMBL-ABR: an interview with Malvika Sharan

This week we interview EMBL Computational Biologist, Malvika Sharan on the subject of Open Science. Her view is that there are ways for biologists to protect their intellectual property and still contribute to Open Science using the example of biorXiv, which allows pre-publication archiving and distribution of manuscripts and data related to biosciences. Full interview.

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Global Organisation for Bioinformatics Learning, Education & Training (GOBLET) Jan 2017 news out now

Get full update on GOBLET AGM held in Brisbane in late 2016 and other news from the Bioinformatics learning community: January newsletter

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EMBL-ABR: an interview with Michael Hoffman

University of Toronto’s Michael Hoffman muses on Open Science for us this week. He sees Open Science as vital to making any progress in bioinformatics: “those developing bioinformatics methods often rely on freely available data, and those analysing data often rely on freely available methods. The speed of progress in bioinformatics has only been possible

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EMBL-ABR: an interview with Stephen Eglen

Asked how a network such as EMBL-ABR might encourage Open Science for Australian biosciences this week’s interviewee, Cambridge’s Stepen Eglen, answers: “I am cautious of adding more infrastructure (hardware, databases, websites) to support open science activities at a national/institutional level. I would hope instead that EMBL-ABR adopt and support existing international infrastructure wherever possible. It is

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Working with EMBL-EBI to extend the impact of Australia’s Antibiotic Resistant Pathogens project

In January 2017, Sandra Orchard, Molecular Interactions Team Leader, European Bioinformatics Institute (EMBL-EBI) based at the Wellcome Trust Genome Campus at Hinxton in Cambridge was pleased to welcome Deputy Director EMBL-ABR, Vicky Schneider, who will be based with them while she works on building relationships across our two enterprises. Sandra said, “I’m thrilled to welcoming an old

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2017 Interview Series: reflecting on Open Science & Bioinformatics

Open Science and Bioinformatics is a key theme for our Interview Series in 2017: Michael Hoffman, Toronto, Canada Stephen Eglen, Cambridge, UK Malvika Sharan, EMBL, Germany Rochelle Tractenberg, Washington, USA Rob Lanfear, Canberra, ACT, Australia Jeff Christiansen, Brisbane, Qld, Australia Saravanan Dalayan, Melbourne, Vic., Australia Graham King, Lismore, New South Wales, Australia David Lynn, Adelaide,

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EMBL-ABR: an interview with Richard Edwards

Richard Edwards is the developer of SLiMSuite, an open source bioinformatics tool for the prediction of short linear motifs (SLiMs) and related sequence analysis. At his lab, they are particularly focussed on the molecular basis of evolutionary change and how analysing the genetic sequence patterns left behind may make useful predictions about contemporary biological systems. 

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EMBL-ABR: an interview with Jyoti Khadake

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Jyoti Khadake was in Melbourne recently as International Faculty on the Data Life Cycle workshop series, as our expert on microbial genomic data and data accessibility and challenges. As someone who works in biomedical research, she sees the social and ethical considerations vary greatly amongst bioinformaticians, depending on their area of study, but that they all

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EMBL-ABR: an interview with Kate LeMay

Kate LeMay works at the Australian National Data Service as a Senior Research Data Specialist, focusing on health and medical data. She was in Melbourne last month to attend our EMBL-ABR workshops. We asked her about bioinformatics in general and the data life-cycle in particular. Her message is clear: using a framework like the data life

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EMBL-ABR: an interview with Lavinia Gordon

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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

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Dr Dieter Bulach

EMBL-ABR network: an interview with Dieter Bulach

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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

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New Galaxy Australia community opens registrations for GAMe 2017

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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

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Prof Rudi Appels IWGSC

EMBL-ABR network: an interview with Rudi Appels

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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

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EMBL-ABR network: an interview with Sandra Orchard

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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

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Australia now Biosharing through agreement finalised this week

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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

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EMBL-ABR: an interview with Jenny Martin

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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

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GOBLET / EMBL-ABR agreement to build international alliances

With a collaborative agreement being formalised this week between EMBL-ABR and the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET), we are very pleased to have Professor Teresa Attwood, founder, and current Chair of GOBLET, musing on current trends and needs in bioinformatics. Her vision for EMBL-ABR?  To see it become the go-to Hub for Australian bioinformatics,

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EMBL-ABR: an interview with Suzanna Lewis

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This week’s interviewee Suzanna Lewis proposes nothing less than a revolution in research publishing orthodoxy where you get credit for the fact that someone can easily find and re-incorporate or integrate your information and where then the task of data curators moves from tidying up data to reviewing and synthesising it. Read more.

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2016 Interview Series: reflecting on bioinformatics

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During 2016 we have contacted Australian and international expert bioinformaticans and asked them the same six questions. The variety of their responses reflects the diversity of our community and the challenges we face. Take some time to read them here: Professor Mark Ragan, Queensland, Australia Professor Marc Wilkins, News South Wales, Australia Dr Jac Charlesworth, Tasmania,

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Welcome to the data commons

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On June 7 HealthcareITNews led with the headline, Joe Biden unveils precision medicine database at University of Chicago. The report documents how a new Genomic Data Commons is pulling data from US National Cancer Institute programs of over two petabytes of cancer genomic datasets, making it accessible to a wider research community. EMBL-ABR’s interest is

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EMBL-ABR: an interview with Frederik Coppens

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Philippa Griffin, our Open Data Coordinator, has been at Indiana University, Bloomington, Indiana, USA, as one of a team of instructors at the Galaxy Community Conference 2016. While there she had the opportunity to interview some leading practitioners from our global network of bioinformaticians. For this week’s interview she spoke with Frederik Coppens from Belgium.

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EMBL-ABR network: an interview with Allegra Via

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Trained as a theoretical physicist, Allegra Via was lured by the beauty of proteins into the life sciences, and using her unique skills, gravitated towards bioinformatics. She regularly teaches Bioinformatics and Python Programming Language to bioinformaticians and biologists and in 2010 she created the “Bioinformatics using Python for Biologists” course for the Gulbenkian Training Programme

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EMBL-ABR network: an interview with Rafael Jimenez

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This week we hear from Rafael Jimenez, who is working at the coalface of life science data infrastructure as Chief Technical Officer, ELIXIR Hub, based in the UK. Rafael sees the need for faster adaptation to this big data era where we need to find new ways to fund, sustain and continue to develop the many useful

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EMBL-ABR network: an interview with Pedro Fernandes

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In this week’s interview, we have a perspective from Portugal, but it could be from anywhere in the world. When asked what is missing in bioinformatics AND life sciences, Pedro Fernandes lists three things: 1. a better balance between formal and continuous non-formal education 2. lowering of barriers to access data and computational resources 3. greater standardisation

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EMBL-ABR network: an interview with Nathan Watson-Haigh

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In a multi-disciplinary field such as bioinformatics, it is not possible to be an expert in everything. We bioinformaticians cannot expect life scientists to leave the lab behind completely to gain expertise in bioinformatics. Similarly, bioinformaticians cannot be expert biologists, computer scientists, software developers etc. It takes a team of bioinformatics, each with expertise in

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EMBL-ABR network: an interview with John Hancock

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Asked recently for his views on the current state of bioinformatics, the Head of the ELIXIR UK Node based at The Genome Analysis Centre in Norwich, Dr John Hancock, highlighted open data as an essential pre-requisite for modern bioscience and that it is definitely not something to be afraid of. Read more.

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EMBL-ABR network: an interview with Jason Williams

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The US National Cyberinfrastructure for Life Science (CyVerse) is a US National Science Foundation funded project supporting a community of more than 30,000 users at every level of bioinformatics experience (from little-to-no bioinformatics training to power user). As Education, Outreach and Training lead for CyVerse, Jason Williams spends a lot of time teaching wet-lab biologists to become

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EMBL-ABR network: an interview with Jac Charlesworth

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Tasmania has a small but vibrant bioinformatics community and one of its very active members is Dr Jac Charlesworth, who runs a computational genomics research group at the Menzies Institute for Medical Research at UTAS. She also manages the computational infrastructure for genomics research at Menzies, and provides bioinformatics training and support. Asked what she wants

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EMBL-ABR network: an interview with Marc Wilkins

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Another key person in bioinformatics in Australia who our Deputy Director Assoc Prof Vicky Schneider met with on her recent trip to three States was Prof Marc Wilkins in New South Wales. Marc wants EMBL-ABR to raise the profile of bioinformatics in Australia, to help coordinate and facilitate activities and to share know-how. The more support we can

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April 2016 news update

It has been a busy few months here in the EMBL-ABR Hub. Dr Jason Williams came to Melbourne to present a workshop on CyVerse, and to discuss possible routes for collaborations, including a federated model of CyVerse for Australia. Full schedule and details of Jason’s CyVerse workshop. Earlier in the month Deputy Director Vicky Schneider visited three Australian

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EMBL-ABR International Science Advisory Group

EMBL-ABR International Science Advisory Group brings together a number of highly-regarded scientists from around the world, to discuss and advise on EMBL-ABR strategy, activities and priorities. Read more.

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EMBL-ABR Network: an interview with Mark Ragan

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On her recent visit to meet key bioinformaticians around the country, our Deputy Director Assoc Prof Vicky Schneider was keen to ask people what they thought some of the collective actions EMBL-ABR could take to support bioinformatics in Australia. In Queensland, Prof Mark Ragan said he wants to see biology mature as a data science through a

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Why big data is a big deal

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The following is an extract from “Why Big data is a big deal” featuring EMBL-ABR Director Andrew Lonie and Deputy Director Vicky Schneider “…University of Melbourne Associate Professor Vicky Schneider is the new deputy director of theEMBL Australia Bioinformatics Resource (EMBL-ABR) hosted at the Victorian Life Sciences Computation Initiative (VLSCI) and is part of this

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Intensive training in Cancer Genomics and the Genome Analysis Tool Kit in Melbourne

Two of the latest instalments of Bioplatforms Australia training workshops have been held in Melbourne and Sydney in February. The GATK Best Practice course brought the Broad Institute’s Geraldine van der Auwera to the University of New South Wales and the University of Melbourne. A new 3-day Cancer Genomics workshop was run in the Melbourne

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