Author Archives: Helen van de Pol

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Training: an interview with Gareth Price

Category : interviews , training

Gareth Price has years of experience wrangling his own and other life scientists’ research data. He doesn’t want to see good data go to waste or see unskilled researchers struggling with their data, so training is very high on his agenda. His involvement in our Galaxy Australia project supports these goals. In this interview, he shares his comprehensive view of the current life science data landscape with regard to bio-molecular data and explains why he cares about what EMBL-ABR is trying to do.

Full interview.


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EMBL-ABR 2017 Annual Report now online

Category : news

May 2018

Our hard work over 2017 has been colourfully documented and is now available here ONLINE and as print copies. Below are reflections on the year from our key leaders:

Mr Jason Williams

Chair, International Scientific Advisory Group (ISAG)

It’s my pleasure to convey the International Science Advisory Group’s congratulations on the progress the EMBL-ABR hub and network has made over the past year. The presentation by Dr Ute Baumann – of the new Adelaide node – at our year-end ISAG call made it clear that there is an important role for the activities EMBL-ABR supports, and that the community believes in the value of these activities. Key to EMBL-ABR’s success is its strategic vision to serve as a national network with global connections – unifying and enhancing the efforts and success of its members. We truly believe EMBL-ABR can accomplish this vision.

At the 2016 All Hands meeting the following priorities were identified for 2017: to build relationships with international bioinformatics efforts to generate more activity around training, data, tools and standards; to deliver more tangible outcomes for the nodes; and, among other things, to grow the network. I am pleased to report on behalf of the ISAG that 2017 was a year in which significant progress has been made towards these goals.

Particular credit for these achievements must be paid to Vicky Schneider, whose vision and efforts generated so much energy and cooperation.

The ISAG was particularly pleased to see a successful trial of the hybrid method of delivering Australia-wide workshops featuring international experts; the ongoing work to list Australian training on the TeSS database; greater representation on international efforts such as GOBLET and ISCB; and, the addition of two important new nodes. These activities should serve as models for future achievements. We look forward to EMBL-ABR and its network members continuing to engage and expand because these collaborations are ultimately foundations for collaborations that enhance Australia’s capability to deliver high impact science in areas such as agriculture, biomedicine, and biodiversity.

For 2018, one major focus is to find the most efficient and effective ways to serve the ever-growing demand for skills and resources in the wider life science community, while continuing to address the needs of professional bioinformaticians. As always, the ISAG looks forward to seeing how this vision evolves in 2018 and offers our full support.

Assoc Prof Vicky Schneider

Deputy Director to June 2017

The year started well with the addition of the University of Adelaide as our 11th node. This was followed later in the year by Southern Cross University, making a total of 12 at the end of 2017.

It was excellent to see colleagues invited onto international committees such as Saravanan Dalayan (Metobolomics Australia node) on the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET) Standards Committee and Sonika Tyagi (Monash node) in their Learning, Education and Training Committee. Simon Gladman (Melbourne Bioinformatics node) also joined me in meetings with EBI and ELIXIR in the UK, particularly to discuss ways the Australian-made Genomics Virtual Laboratory might be deployed across Europe.

My special thanks to my colleague, Monica Monez-Torres for helping EMBL-ABR achieve one of the major objectives for 2017, a hybrid model of workshop delivery which I followed with interest from my new workplace in the UK. Congratulations to all involved in making this work, it certainly demonstrated what can be achieved from greater cooperation across this growing network. In 2017 our social media presence grew by 63%, new visitors to the website by 69% and newsletter subscribers by 25%. Thank you to many colleagues who agreed to be interviewed for our Open Science Interview Series, which gave a broad perspective to how important open science is to the practice of bioinformatics.

We also published three journal articles during the year: Griffin et al, Best practice data life cycle approaches for the life sciences, F1000Research, August 2017, which documented the collaborative efforts of those involved in the 2016 EMBL-ABR Data Life Cycle workshops; Schneider et al, A global perspective on evolving bioinformatics and data science training needs, Briefings in Bioinformatics, August 2017; and, Schneider et al, Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia, Briefings in Bioinformatics, June 2017.

These findings informed the priorities given to the Key Area activities of Compute, Data, (International) Standards, Platforms, Training and Tools.

My congratulations to all for a great effort and I look forward to following the progress of EMBL-ABR in 2018.

Assoc Prof Andrew Lonie

Director

A highlight of 2017 was ending the year with the All Hands meeting hosted by Prof Marc Wilkins at the SBI node at the University of New South Wales. At that meeting we discussed our shared vision for an Australian Biosciences Data Capability (ABDC) which incorporates a lot of what we are already doing through EMBL-ABR, or are planning to do. I must thank Vicky Schneider for her contributions to the establishment and launch of EMBL-ABR over 2016-7. Vicky left us in the middle of the year with a great deal in place and a strong vision of what we might become as a network.

On our website now we describe ourselves as a backbone organisation delivering collective impact for the biosciences in Australia. This term comes from Turner et al, Understanding the Value of Backbone Organisations in Collective Impact, Stanford Social Innovation Review, July 2012. To demonstrate shared success and collective impact they ask some key questions:

Would this work be carried out by individual organisations/researchers in the same time frame?
We don’t believe so. Instead, world-class Australian researchers have been co-opted to activities which help to share their expertise across the research community.

Has the vision of the project now shifted to see a developing role for it in the future?
EMBL-ABR has certainly helped demonstrate and inform the lobbying efforts for the ABDC, which we expect to help secure funding for life sciences digital infrastructure.

Is there a role for the project in feeding back to users data from the project which in turn aids further community development?
Surveys, publications, interviews and training evaluation data have all been made available to the bioinformatics community across Australia and this is helping to form new collaborations and streamline training efforts to help deal with Australia’s tyranny of distance. Surveys carried out at the hub have provided important data which has affirmed the growing frustration in the research community for the lack of skills and the complexity of dealing with data. This has helped to set priorities for future action but also informed lobbying approaches for further infrastructure funding.

Can the project be used as an example to explain to the public the value of investment in these, often, invisible processes?
Infrastructure initiatives which support researchers to make their research data more accessible by industry, government and the wider community, not just expert bioinformaticians, is a major objective of the open science movement. Our network is currently focussed on projects which will generate community value in the fields of health, the environment and agriculture and 2018 will see an increase in this work.

For 2017, my special thanks goes to our esteemed ISAG for their sustained advocacy, support, advice and hard work and particular thanks to our co-funders, Prof James McCluskey, DVC/R, University of Melbourne and Mr Andrew Gilbert, General Manager, Bioplatforms Australia. Our further thanks to the University of Melbourne’s Faculty of Medicine, Dentistry and Health Sciences who host the EMBL-ABR Hub via their support for Melbourne Bioinformatics.

We are already well-advanced with our plans for 2018 and hope that we’ll be engaging with many of you as we work to deliver more collective impact for the biosciences research community in Australia.

Yours sincerely

Assoc Prof Andrew Lonie, Director
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Available here ONLINE. 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, Open Data, Open Source: 21st century research skills for life scientists

Open Science, Open Data, Open Source is published by colleagues in the EU.

Its introduction offers: 

The goal of this resource is to give a bird’s eye view of the developments in open scientific research. That is, we cover both social developments (e.g. the culture in various communities) as well as technological ones. As such, no part of the contents are especially in-depth or geared towards advanced users of specific practices or tools. Nevertheless, certain sections are more relevant to some people than to others.

Audiences include:

  • Graduate students 
  • Lab technicians 
  • Data scientists
  • Principal investigators 
  • Scientific publishers 
  • Science funders and policy makers 
  • Science communicators.

 


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Training: an interview with Sonika Tyagi

Category : interviews , training

Training is one of the key focus area for the EMBL-ABR and its effort to network with various Australian institutes who develop and run bioinformatics training activities is going to help in standardising, sharing and reusing bioinformatics training resources. EMBL-ABR’s affiliations with international bodies such as GOBLET, ELIXIR, NIH-BD2K, BD2KTCC etc. will help us keep pace with international best practices in training standards and programs.

Full interview.


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Making Australia’s unique soil and marine microbiome data more accessible for all

Category : news

This month work started on the Australian Environmental Microbiome Research Data Cloud project which will link significant national soil and marine datasets with national biosciences computational infrastructure and services.

Understanding the combined genetic material of the microorganisms in their environment is of broad national and international utility for academic researchers, industry and government agencies, but at the moment it is only accessible to skilled bioinformaticians and this limits its potential.

Experts from the Centre for Comparative Genomics (CCG), Queensland Cyber Infrastructure Foundation (QCIF), Melbourne Bioinformatics at the University of Melbourne, the Atlas of Living Australia, CSIRO and the EMBL Australia Bioinformatics Resource (EMBL-ABR) will establish a new cloud-based analysis system to make the data easier to find, analyse and interpret.

Full story.


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Training: an interview with Daniel Park

Category : interviews , training

Our first interview in the 2018 series, focussing on Training, is with the University of Melbourne’s Assoc Prof Daniel Park who says: The shortage of bioinformaticians, left unaddressed, will continue to present a serious bottleneck to progress in many areas from discovery to translation. Without serious investment in this area, Australian life scientists will slide in terms of their global relevance except for a relatively small number of well-funded individuals. Without such investment, the substantial majority will become followers and bit-part players rather than leaders on many international consortium-based projects. In terms of clinical applications, we become a consumer rather than a producer, with obvious cost implications.

Full interview.


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2018 Interview Series: Training, training, training

Category : interviews , training

There is good reason we are focussing on training for the 2018 Interview Series:

“A national bioinformatics training infrastructure may be the best strategy to empower researchers to participate in biology’s evolution as a data science,” was one finding in an article published by Jason Williams, Chair our of International Advisory Group, and co-authored with Tracy K. Teal, in the Annals of the New York Academy of Sciences special January 2017 issue on Data Science, Learning, and Applications to Biomedical and Health Sciences. The paper is here: A vision for collaborative training infrastructure for bioinformatics. Earlier in 2017 we invited Jason to elaborate, and he wrote:

Life science research is and will increasingly be shaped by infrastructure that supports it. At the beginning of Big Data biology, this meant funding sequencers and computers and while we still need those, we also need to become smarter. Increases in our ability to solve the big problems in biology have come as much from scaling people (through training, sharing of practices, and collaboration) as they have from cheaper sequencing or faster processors.

Read the views of our invited interviewees:

Daniel Park, Melbourne Bioinformatics, Victoria, Australia

Sonika Tyagi, Monash Bioinformatics Platform, Victoria, Australia

Gareth Price, QFAB Bioinformatics, Queensland, Australia


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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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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.