Author Archives: Helen van de Pol

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EMBL-ABR: an interview with Stephen Eglen

Category : Uncategorised

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 tempting to provide new infrastructure, and might even be possible to get funding to establish new resources. However, long-term maintenance of these resources is a concern, and so I think it is better to pool resources with other current approaches. If you feel something is missing, lobby EMBL/EBI to provide it.”

Full interview.


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

Category : Uncategorised

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 colleague from the protein-protein interaction domain. I worked with Vicky when she was involved with the MINT database and it is great to host her with my team at EMBL-EBI. We will be particularly exploring with EMBL-ABR a specific project that will be useful for making the most of the data and insights generated through the Australian Antibiotic Resistant Pathogens project. The added value gained through having curated information at the interactome level will become tangible as the project data analysis progresses.”

“Our aim is to work together to move towards full coverage of the interactome of the model organism E.Coli K17 in the IntAct interaction database and also a catalogue of the protein complexes present in this bacteria in the Complex Portal with a view to using these to map interologs (interacting homologs) in pathogenic microorganisms of interest to the Australian community,” she explained.

Vicky was equally enthusiastic: “A project such as this represents exactly what I am trying to make happen for my Australian colleagues. To add value to data being generated in Australia by ensuring it is properly curated and maintained, while at the same time demonstrating how this presents a better option than trying to keep them in local, often resource-poor repositories.”

 

Sandra Orchard joined the Faculty of the EMBL-ABR Best Practice workshops held in October 2016. She was also interviewed last year as part of our Interview Series (read her interview here). She is particularly focussed on training in how to make the most of bioinformatics resources for studying networks, pathways, interactions and complexes. She is also a member and Treasurer of the Executive Committee of the International Society for Biocuration and chairs the Molecular Interaction work-group of the HUPO Proteomics Standards Initiative.

 


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EMBL-ABR: an interview with Richard Edwards

Category : Uncategorised

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.  SLiMSuite was developed to analyse these short regions of proteins that mediate interactions with other proteins – to help with this work.
In this interview Richard reflects on bioinformatics in Australia as well as the realities of building a sustainable model for the development and maintenance of useful bioinformatics tools such as his.

 


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EMBL-ABR: an interview with Jyoti Khadake

Category : Uncategorised

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 need to adopt the agreed standards for data curation and management which are being implemented across this discipline.

Full interview.


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EMBL-ABR: an interview with Kate LeMay

Category : data life cycle

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 cycle ensures that Australian bioinformaticians are keeping up with best practice standards being used and developed internationally.

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.