The eight finalists of the Enlighten Your Research 4 contest (EYR4) wrote a blog post about the projects they proposed. This week the post from Jos Kleinjans, Daniel Theunissen and Maarten Coonen (Maastricht University)
Located at the most southern university in the Netherlands in Maastricht, the department of Toxicogenomics is a young and already successful research department. As part of the Faculty of Health, Medicine and Life Sciences, the department of Toxicogenomics (TGX), covers a multidisciplinary team of biologists, chemists, toxicologists and bio-informaticians working in close collaboration to establish the biological impact of exposures to potentially toxic compounds.
The rapid development of the new, so called ‘omics technologies’, has enabled us to measure cellular responses to toxic chemicals at multiple molecular levels with higher sensitivity than most classical effect markers.
At the same time, information on the involved molecular mechanisms of action is provided. As such, toxicogenomics research combines toxicology with genomics approaches in order to obtain more accurate understanding of toxicological processes. The application of these innovative ‘omics technologies’ in in vitro toxicology and human health risk analysis is thus to be regarded as the central research paradigm of our department.
Big data challenge
Currently, we are in the process of switching from the ‘classic’ omics technologies, e.g. micro-arrays, to next generation sequencing (NGS). With the advance of NGS, we have a vast amount of new opportunities for gathering data on toxic responses. But with these new opportunities come new challenges. Especially for the bio-informatics team and our system administrators, who need to deal with the enormous amounts of data. This requires new innovations and concepts, concluding in a real BIG DATA challenge.
Innovative IT solution
To make sure we are future-ready we went looking for novel and innovative IT solutions that enable us to dynamically scale our infrastructure when necessary. This solution was found in the SURFsara infrastructure. In order to get acquainted with this infrastructure, a pilot project was carried out in which a RNA-seq dataset was analysed using the cloud infrastructure. It was during this pilot that we noticed the opportunity to compete in the EYR4 challenge. This challenge would give us the chance to combine the knowledge, infrastructure and ideas of SURFsara and the NLeSC.
NGS data integration and visualization
We then started to write a proposal to take part in the EYR4 challenge. This proposal includes novel ideas to tackle the problem on NGS data integration and visualization. The analysis and visualization will be performed on the infrastructure of SURFsara with the help of the expert support that is offered in this challenge.
Jos Kleinjans – professor, department of Toxicogenomics
Daniel Theunissen – bio-informatics associate, department of Toxicogenomics
Maarten Coonen – bio-informatics associate, department of Toxicogenomics
The department of Toxicogenomics has strong national and international collaborations. They coordinate the Netherlands Toxicogenomics Centre and are involved in numerous EU projects, of which they coordinate three.