BACKGROUND

The Faculty of Natural Sciences and Technology (NT) at the Norwegian University of Science and Technology (NTNU) invites applicants for a PhD research fellowship. This fellowship is in the research area of System Biology. The newly established systems biology group (http://www.ntnu.no/english/systemsbiology/projects) is currently looking for a candidate to work in knowledge management, focusing on bringing together biological information from different sources (databases, websites, experiments, literature) in a format that allows queries and computational reasoning (AI). The biological area is biomedical and focused on Gastrin-mediated signalling. Gastrin is a hormone, mainly produced by G-cells in response to food, and is involved in different regulation mechanisms. Gastrin activates and stimulates processes in the stomach and gut, including growth of specific cells in these tissues. Faulty regulation of gastrin, or hypergastrinaemia can result for example in cancer tumours. The study of the biological pathways involving gastrin and its role in triggering cancer can help to find clues for many cancer types.

RESPONSIBILITIES

Further development of the BioGateway Project (http://www.semantic-systems-biology.org/biogateway), a Semantic Systems Biology approach that will allow advanced queries for hypothesis generation. The candidate will contribute to the work of the knowledge management project, focusing on extraction of knowledge from literature, ontologies and databases relevant for human gastrin response pathways. In addition, the knowledge base will be queried to construct new hypotheses about gastrin response pathway effects on cells and tissue, and these hypotheses will be tested in wet-lab experiments. The work implies the use and further development of software tools to facilitate the knowledge extraction process, this in close collaborations with experimentalists from the gastrin systems biology group at the Department of Cancer Research and Molecular Medicine. The candidate will be steered by both biologists and systems biologists, ensuring that the project will be focused to pertinent and important biological questions relevant for gastrin biology and fundamental concepts (modelling and data integration) of systems biology will form the core of the project.

REQUIREMENTS

The PhD position is for a person skilled in bioinformatics/computer sciences/systems biology. The candidate should have a clear interest in semantic web technologies and ontologies. Software and data format skills necessary for this project include OWL, RDF, OBOF ontologies, Perl.

PREFERENCES

Some experience with Linux, Java, MySQL, PHP will be an advantage.

LOCALE

The work will be done at NTNU, located in Trondheim, Norway.

COMPENSATION

The appointment of the PhD fellow will be made according to national guidelines for appointment of PhD fellows at universities and university colleges and to the general regulations for university employees in Norway.

HOW TO APPLY

Send your CV to kuiper[at]nt.ntnu.no.

DEADLINE

Please respond by 31.11.08