Author Archives: Helen van de Pol

  • 0

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.


  • -

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.


  • -

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.


  • -

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


  • -

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.


  • -

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.


  • -

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.


  • -

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.

_________________________________________________________________________________________

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.


  • -

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.


  • -

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.