Bioinformatics

4 year BBSRC PhD Position Available: start Oct 2015, UK residents only


Living figures: reproducing published experiments in situ

Speaking about the issues thrown up by ‘Big Data’, The Economist reported in the article “Welcome to the Yotta World” that, by 2018, there would be a talent gap of ~150,000 data-science professionals globally. The problem is particularly acute in high-throughput biology. Here, complex environment- and software set-ups are required to support down-stream data analyses; this can have profound consequences not only for how analyses are performed, but also for how results are interpreted and reported in the scientific literature. As a result, scientists often find it impossible to repeat published experiments faithfully. New approaches are therefore required to forge better links between published articles and their underlying data, to help researchers visualise and reproduce the results described in the papers they read.

To make progress in this area, an exciting collaboration has recently been established between The Genome Analysis Centre (TGAC, Norwich) – a leading genome and bioinformatics research facility in Europe – the eLife journal (Cambridge) and the University of Manchester. Combining expert knowledge in visualisation and analysis of high-throughput biological data, the project will exploit the principal technologies developed by partners: the BioJavaScript open-source library for visualisation of biological components; the Utopia Documents ‘smart PDF reader’; and the publishing platform of the innovative, open-access journal eLife. The goal of this PhD is to develop a proof-of-concept open infrastructure, to allow scientists to reproduce computational experiments described in genomics-based research papers. This is an ideal opportunity for an enthusiastic candidate wishing to develop critical skills in the highly marketable area of data science, ultimately to contribute to a new publishing paradigm that will facilitate data analysis in situ.

Based mainly at TGAC, the candidate will gain industrial experience through periodic visits to the headquarters of eLife (the equivalent of 1 month per annum) to work with Ian Mulvany, head of technical development at the journal. Visualisation of genomic data, and their integration with analysis platforms (e.g., Galaxy), will also be an essential part of the project. TGAC’s infrastructure, computing facilities and involvement in high-throughput biological research, coupled with eLife’s innovative publishing practices and Manchester’s smart PDF reader technology, will provide the appropriate technological framework to underpin this novel investigation into reproducibility, and the ideal environment for developing a new generation of easy-to-use tools for interacting with life-science literature.

Apply here:
http://www.tgac.ac.uk/dtp-studentships/living-figures-reproducing-published-experiments-in-situ/

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