Category Archives: news

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Bioinformatics expertise shared across Australian network assists international research collaboration

Category : news

When listening to the needs of research groups around Australia, we hear that bioinformatics challenges come in all shapes and sizes. Sometimes very specific skills are required to solve particular problems sporadically throughout a project, and often the required expertise can’t be found close at hand. The benefits of an informed network that shares knowledge and links people can be particularly important when the needs are geographically distant from the unique and in-demand skills they need.

A nice example of the sharing of skills across borders and the injection of fresh bioinformatics talent into diverse research groups has recently supported the release of a new platform that provides a centralised knowledge-base and analysis platform for cancer protein interaction networks. Connections made between a junior bioinformatician training in Melbourne and a prestigious research lab in Adelaide have helped to deliver on an internationally funded and highly collaborative project.

MSc(Bioinformatics) student at the University of Melbourne and Melbourne Bioinformatics casual worker, Priyanka Pillai, met Prof Robert Saint, Deputy Vice-Chancellor (Research) at Flinders University, South Australia, while volunteering at the Digital Hospital Design booth at the digital health and informatics conference, HIC 2016. Prof Saint referred this keen student to Associate Prof David Lynn who is an EMBL Australia Group Leader in Biomedical Informatics and Immunology in the Infection and Immunity Theme at the South Australian Health and Medical Research Institute (SAHMRI) and at Flinders University.

As part of an EU funded project, Assoc Prof Lynn had a website and database already developed by a Senior Software Engineer, but was needing a visualisation app to complete the project, publish the work and offer the portal for public use. With a wealth of practical work experience already under her belt, Priyanka was offered a three-month bioinformatics summer internship starting December 2016.

Her role was to develop a web application tool for the PRIMESDB portal: http://primesdb.eu/. PRIMESDB is a systems biology platform that facilitates the collection, annotation and integration of data generated from the Protein interaction machines in oncogenic EGF receptor signalling (PRIMES) project. This 13 partner Collaborative European FP7 Health project investigates the role of protein interactions in health and diseases, making use of proteomics, mathematical modelling and genomics to understand the role of protein-protein interactions (PPI). The focus of the project is on oncogenic signalling in the EGFR pathway, which is particularly of interest in the study of drug targets for colorectal cancer. To investigate the PPI network, more than 90 bait proteins and their interacting prey proteins were studied. The web application that Priyanka developed allows users to interactively visualise 93 PRIMES EGFR network bait proteins and their interactions.

Priyanka worked closely with Assoc Prof Lynn and Dr Sriganesh Srihari, and sought essential assistance from colleagues at Melbourne Bioinformatics. As part of her earlier Masters course, Priyanka’s research project was co-supervised by Melbourne Bioinformatics staff, and her work at training events and conferences had exposed her to a broad network of Melbourne Bioinformatics staff including those with useful bioinformatics software development skills that she could call on as needed. Her SAHMRI internship eventually extended into a research assistant/ developer role to add additional features in the web application. A publication will follow shortly.

Her time with the Lynn EMBL Australia Group offered Priyanka the opportunity to interact with highly distinguished researchers from computational statistics, immunology, biochemistry, systems biology, biomedical informatics, microbiology, proteomics and genetics. Her work at SAHMRI enriched the postgraduate training she had undertaken, and the project benefited from Priyanka’s expertise and valuable network of highly skilled bioinformaticians. She said,

The fantastic opportunity of a bioinformatics internship and exposure to so many talented researchers was the best professional break a student researcher could ask for.

The opportunity to be a part of such multifaceted and interconnected research projects left Priyanka eager to find a fresh challenge to apply her skills to. Now back in Melbourne with an established network of trusted colleagues in South Australia, Priyanka is actively working towards a new opportunity in the Melbourne biomedical precinct in the area of infection and immunity.


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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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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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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.