Odefy

Odefy is a freely availabe software package for the automated conversion of Boolean models to systems of ordinary differential equations (ODEs). It can import Boolean models from several sources and generate ODE systems in various external formats. Furthermore, Odefy contains methods for the analysis of both Boolean and ODE-transformed models. For detailed information about the conversion method, please refer to Wittmann et al., 2009.

Requirements

For full functionality, Odefy requires MATLAB version 7 or higher. All functions that do not require a graphical user interface are also compatible with the free GNU Octave software package.

License

Odefy is free for academic and non-commercial purposes. Read full license

Quickstart

A one-minute introduction to Odefy simulations. Click here

User's guide

1. Modeling frameworkExplains the basics of Boolean modeling and the ODE transformation process
2. Model creationOdefy can generate Boolean models from Boolean equations and from graphs created using the yEd graph editor. Alternatively, models can be imported from CellNetAnalyzer, GINSim or the PBN toolbox.
3. Model simulationHere you learn how to perform Boolean and continuous simulations using both the Odefy GUI and the command line
4. Model exportingOdefy models can be exported to different external formats, including GNA, the PBN toolbox, SQUAD, MATLAB .m files, R, the SBML format and the SB toolbox
 
5. Function overviewAn overview of all functions implemented in the Odefy package

Odefy by CMB, http://cmb.helmholtz-muenchen.de/odefy