Author Archives: Helen Gardiner

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Open Science: an interview with Jeff Christiansen

Category : interviews , open science

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 insights into open science.

Jeff knows that the whole ecosystem of data, tools and compute that is used in research is very complex and spans not only national and local resources but also many international and also commercial resources. He believes it makes sense to resource national efforts to increase/improve local infrastructure and efforts to better connect Australian researchers into this global ecosystem.

And when asked how new biologists should handle their data he challenges: first think about developing systems and methodologies to describe experimental inputs, methods and outputs that would enable you to share this information with your ‘future self’. Indeed!

Full interview.

 

 


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EMBL-ABR 2016 Annual Report now online

Category : news

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 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

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


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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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