Author Archives: Helen van de Pol

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

Category : GOBLET

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

Category : Uncategorised

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 due to the availability of open data and methods.”

Full story.


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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.