Odefy

Odefy converts Boolean models into systems of ordinary differential equations (ODEs) to enable quantitative analysis of regulatory and signaling networks.

Key Features:

• Automated transformation: Automates conversion from Boolean models to ODEs using multivariate polynomial interpolation and optional sigmoidal Hill functions.
• Input compatibility: Accepts sets of Boolean equations, graph representations of Boolean networks, and models imported from CellNetAnalyzer, GINSim, and the PBN toolbox.
• Export and interoperability: Exports models to SQUAD, GNA, MATLAB script files, SB toolbox, SBML, and R script files.
• Environment compatibility: Compatible with MATLAB and Octave.
• Simulation and visualization: Provides basic simulation and visualization functionalities for both Boolean and continuous models.
• Scalability: Implements a standardized method applicable to large networks.

Scientific Applications:

• Systems Biology: Enables quantitative analysis of regulatory and signaling networks that originate from qualitative Boolean models, capturing time courses and concentration levels.
• Stem cell differentiation: Applied to a mutual inhibitory switch involved in stem cell differentiation to analyze quantitative dynamics.
• Developmental patterning: Applied to a regulatory network governing spatial expression at the mid-hindbrain boundary to investigate quantitative spatial dynamics.

Methodology:

The transformation uses multivariate polynomial interpolation to convert logical operations into continuous dynamics represented by ODEs, with optional sigmoidal Hill functions; the method is standardized and applicable to large networks.