Bioinformatics expertise shared across Australian network assists international research collaboration

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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.