Author Archives: Helen van de Pol

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Developing an Australian Biosciences Data Capability – October 2017 update

Category : news

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 have a variety of data needs and a variety of skills, and they will increasingly be interacting with both local and global resources.

So, questions arise such as: What infrastructure and activity is needed now to support all to do world-class science? Within our Australian funding context (in particular, the NCRIS Roadmap), what should we prioritise to give us the greatest leverage to access international resources and collaborations? How might we anticipate the kind of transformative science envisaged in a more data-intense future?

At the EMBL-ABR All Hands meeting held in Melbourne late in 2016, key people working across data, infrastructure and bioinformatics discussed the future needs for biosciences data capability (digital data, digital tools (software), cloud technologies and compute infrastructure) with members of the existing EMBL-ABR International Scientific Advisory Group (ISAG). Bioplatforms Australia then provided funding to contract Rhys Francis (author, NCRIS eResearch investment/super science plans (2007-10) and the draft eResearch Framework (2013-15)) to work with me to establish a framework, a plan, a process. Our ideas have since been ‘road tested’ at a large workshop with Queensland-based research leaders held in Brisbane earlier this month and more workshops are being planned for other States. We are also gathering a National Reference Group of high profile domain-specific researchers to act as guides and advocates. This group is meeting online in October in preparation for discussions with government in Canberra in late November. Concurrently we are testing our proposals with our experts on the EMBL-ABR ISAG.

We want to keep everyone informed about this process and this will generally be through the EMBL-ABR communication channels. So please sign up for EMBL-ABR news at www.embl-abr.org.au to get all updates.

If you wish to contribute to these discussions, or know how your institution or research is being represented in this process, please email alonie@unimelb.edu.au.


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Open Science: an interview with David Lynn

Category : interviews , open science

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 research in immunology, and he is quick to acknowledge that the shared resources of others were essential to that. So Open Science is a concept he supports, but he says it needs appropriate incentives to work: “Right now, most assessment of scientific impact (e.g. for grants, promotion, etc) is based on the quantity and quality of publications. Researchers frequently do not formally cite the bioinformatics software they use. We need to ensure that high-quality, well-supported code, software and data are appreciated and considered when considering impact. We therefore need agreed metrics to do this and to weight them similarly to traditional citations. If done properly this will further incentivise, open, well-supported data and resources.”

Full interview.


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

Category : data life cycle , news

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 our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a ‘life cycle’ view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on ‘omics’ datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.

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The paper was led by Pip Griffin and Vicky Schneider with a number of co-authors including our Key Area Coordinators Group and Activity Leads and workshop faculty (local and international) and participants.

Go here for further details about these workshops.


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Open Science: an interview with Graham King

Category : interviews , open science

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 where Australia’s experience is based upon our unique flora and fauna and our challenging physical environment. “This will also give us access to knowledge generated elsewhere,” he says. “We need to work closely with CyVerse and Elixir… don’t re-invent the wheel or duplicate investment elsewhere….”

Full interview.


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Open Science: an interview with Saravanan Dayalan

Category : interviews , open science

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 interview.


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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.