Author Archives: Helen Gardiner

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Open Science: an interview with Rob Lanfear

Category : open science

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, in which the instrument and data themselves change almost every month. To be at the cutting edge of this field requires almost daily updates on everything from lab protocols to the final data analyses. Traditional publication cycles are far too slow to be useful here. Instead, the community is fantastically open. People are sharing their protocols on sites like www.protocols.io, writing detailed blog posts on tips and tricks for analyses, releasing bioinformatics code early and often on GitHub, and posting preprints as soon as an analysis is complete. Bioinformatics plays an absolutely key role here.

Full interview.


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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 Malvika Sharan

Category : open science

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

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.