Vacancies

Programmer data visualization

A metabolomics support platform will be established as a collaboration between NBIC and the Netherlands Metabolomics Centre (NMC) using the infrastructure of the Virtual Laboratory for e-science. Scientific programmers associated with this platform will closely collaborate with VL-e/SARA to establish this support platform. The programmer will actively participate in the NBIC/NMC programmers network and will obtain a relevant e-(bio)science training.

The University of Amsterdam is one of the core partners of the NMC dedicated to developing new metabolomics data analysis methods. Of vital importance for the translation of data analysis results to biological practice is to visualize these results. To this extend, visualization tools are needed and will constitute an essential part of the support platform.

To meet this visualization challenge we are looking for someone who can help us to visualize large data sets and complex results. The successful applicant has experience with visualization tools and knows how to present our data in an attractive and intuitive way. He or she has a HBO, Bachelor or Masters degree, and has affinity with research in the natural sciences. Experience with web services and workflow management systems, programming (C, Java, Python, Perl and/or Shell programming) and/or experience with bioinformatics/biostatistics software (R, Matlab) will be especially welcome. Needles to say that our new group member possess excellent communication skills.

This is a temporary appointment for 3-4 years, the salary will be in relation to qualifications and experience.

Contact and application

For more information, please contact Dr. Gooitzen Zwanenburg, tel. 020-5256547, e-mail

An application including CV can be submitted to Dr. Gooitzen Zwanenburg

Two full time PhD positions, appointment for 4 years

Description of the positions

Systems biology is rapidly developing as the scientific approach to understand complex biological systems consisting of a large number of components and their interactions. In systems biology, the bottom-up approach uses targeted experiments (focusing on a single metabolic reaction) with a lot of prior knowledge to estimate model parameters. This then evolves towards whole network models. The top-down approach aims at global (system wide) experiments and by using data analysis methods find functional modules that can lead to a better understanding of the underlying system. Incorporating prior biological knowledge will guide the solutions to become biologically relevant.

In this project we aim to build top-down systems biology models by combining explorative data analysis and prior information of the biological system. The biological system we will examine here is the polyphenol degradation pathway. Polyphenols are plant secondary metabolites, ubiquitous in fruits, vegetables, tea and wine that have a role in the prevention of e.g. cardiovascular diseases, metabolic syndrome, etc. Their bioavailability however depends strongly on the variety of gut bacteria that break down the large aromatic molecules into smaller and simpler phenolics that are absorbed into the human body. Some of these phenolics are measured in blood and urine but it is not yet possible to deduct which degradation pathways were used.

The first PhD project focuses on building the knowledge base of polyphenol degradation routes in humans using concept maps. The knowledge base should contain information on the different phenolics that are measured in plasma and urine, their connectivity, regulation, liver conjugation and kidney clearance effects. Furthermore we will explore how to build systems biology models using the knowledge base. Finally we will explore how to validate the knowledge base using systems biology model results. The second PhD project focuses on developing "grey" model methodology that combines data driven models and relevant prior information to build systems biology models. Grey models are a good compromise as they give a good fit to the data and can be interpreted well. The main research questions are how to incorporate various types of prior knowledge in these models and how to validate the grey models. The grey model tools will then be used to build a top-down systems biology model of the polyphenol degradation pathways, giving the possibility of phenotyping individuals.

The projects are funded by the Netherlands Bioinformatics Centre (NBIC) and by the Netherlands Metabolomics Centre (NMC) and performed in collaboration with Unilever.

Requirements for both positions

  • MSc in bioinformatics or biostatistics
  • Strong affinity for data analysis and mathematical models (position 2)
  • Experience with information management (e.g. data bases, programming skills) (position 1)
  • Ambition to perform pioneering research in a developing field of science.
  • Good communicative skills, a multidisciplinary mindset and flexible personality.

For more detailed information regarding these positions you are invited to contact: Dr. Johan Westerhuis, phone +31 20-5256546, e-mail , or Dr. Andrew Gibson, phone +31 20-5257061, email (especially for position 1)