Odefy -- From discrete to continuous models

Background: Phenomenological information about regulatory interactions is frequently available and can be readily converted to Boolean models. Fully quantitative models, on the other hand, provide detailed insights into the precise dynamics of the underlying system. In order to connect discrete and continuous modeling approaches, methods for the conversion of Boolean systems into systems of ordinary differential equations have been developed recently. As biological interaction networks have steadily grown in size and complexity, a fully automated framework for the conversion process is desirable. Results: We present Odefy, a MATLAB- and Octave-compatible toolbox for the automated transformation of Boolean models into systems of ordinary differential equations. Models can be created from sets of Boolean equations or graph representations of Boolean networks. Alternatively, the user can import Boolean models from the CellNetAnalyzer toolbox, GINSim and the PBN toolbox. The Boolean model...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Jan Krumsiek, Sebastian Pölsterl, Dominik M. Wittmann, Fabian J. Theis
• Keywords: BMCBI 2010, Boolean Models, Systems, Toolbox