Vacancies

Scientific Programmer (systems biology)

Systems biology is rapidly developing as the scientific approach to understand complex biological systems consisting of a large number of components and their interactions. Experimental information about the components of the system and their interplay is used to develop and test mathematical models. The experimental work, biological knowledge and experimental data and computational models are cornerstones in an iterative cycle of data-driven modelling and model-driven experimentation in the Netherlands Consortium for Systems Biology, NCSB.

A systems bioinformatics project is defined as part of the NCSB programme. In this project five bioinformatics centers collaborate to provide bioinformatics support to NCSB systems biology projects through the development of methods for data and knowledge management and through development, exchange, and computation of models. This bioinformatics project in turn entails collaboration with several experimental projects in the consortium. This project is also part of the BioAssist programme of the Netherlands Bioinformatics Centre, NBIC.

As part of the systems bioinformatics project the scientific programmer will work on the BioExpert project. The overall aim of the BioExpert project is to develop a framework to represent, integrate and present (curated) knowledge of specific biological systems and to use this information in subsequent modelling applications. The overall framework is based on state-of-the-art approaches for Information Management (e.g., RDF/OWL) and novel approaches for information (re)presentation (i.e., concept map network). The BioExpert knowledge base stores conceptual models that provide a comprehensive, accurate, and up-to-date description of selected biological systems to serve as input for mathematical modeling.

Tasks

Your main tasks are (a) acquisition of domain knowledge (biological, models, parameters, etc.) for selected biological systems, (b) representation of this information in the current RDF/OWL framework, (c) construction of concept maps to (re)present this information (d) integration with systems biology markup languages (e.g., SBML, CellML, KiSAO, Teddy, SBO) and modeling environments, (e) further development of the BioExpert application (user interface, navigation/querying, web-services to access data, visualization, etc.) to enhance its use in systems biology.

Requirements

We are looking for an enthusiastic candidate with a background in (bio)informatics and or biology with a strong interest in information management research. The candidate is willing to combine research with substantial tasks in knowledge acquisition and software development in order to develop BioExpert into a functional systems biology tool.

The candidate should meet the following requirements:

  • PhD in a relevant scientific discipline (e.g., (bio)informatics).
  • Experience with information management research.
  • Excellent software developer (Java, Java frameworks (J2E, JENA, AJAX), web-applications/services).
  • Experience with systems biology markup languages (e.g., SBML).
  • Sufficient social skills to perform optimally in a dynamic scientific team and willing to collaborate with colleagues from other NCSB groups.

For more detailed information regarding these positions you are invited to contact: Prof. A.H.C. van Kampen +31 (0)20-566 7096, e-mail