Odefy

Odefy

Introduction

The understanding of regulatory and signaling networks has long been a core objective in molecular biology. Knowledge about these networks is mainly of qualitative nature, which allows the construction of Boolean models, where the state of a component is either 'off' or 'on'. While often able to capture the essential behavior of a network, these models can never reproduce detailed time courses of concentration levels. Nowadays, experiments yield more and more quantitative data. An obvious question therefore is how qualitative models can be transformed into quantitative ones in order to explain and predict the outcome of these experiments.

Odefy is a MATLAB and Octave compatible toolbox which a modeling technique called HillCube (Wittmann et al., 2009), a canonical method to convert boolean models into continuous ordinary differential equation (ODE) systems. HillCubes are based on multivariate polynomial interpolation and incorporate Hill kinetics which are known to provide a good approximation of the synergistic dynamics of gene regulation.

Toolbox overview


(click to enlarge)

Screenshot

Odefy graphical user interface. The simulation dialog, the export dialog and an exemplary simulation result of a cell cycle model:


(click to enlarge)

Model definition, import & export

Odefy models can be created from sets of boolean equations or built in the yEd graph editor. Alternatively, Boolean models can be imported from the CellNetAnalyzer toolbox, GINsim and the PBN toolbox.


(click to enlarge)

Models can be exported to MATLAB ODE .m files, the Systems Biology toolbox (SBTOOLBOX), the SBML format and the R computing environment.


Download

Current version: 1.18
Download Odefy (407 kb)

License
Version changes


Contact

For suggestions or help requests, please contact


References

  1. Krumsiek J, Poelsterl S, Wittmann DM, Theis FJ. Odefy - From discrete to continuous models. BMC Bioinformatics. 2010, 11:233. [Link]

  2. Wittmann DM, Krumsiek J, Saez-Rodriguez J, Lauffenburger DA, Klamt S, Theis FJ. Transforming Boolean Models to Continuous Models: Methodology and Application to T-Cell Receptor Signaling.<span class="journalname" title="BMC systems biology"> BMC Syst Biol</span>. 2009 Sep 28;3:98. [Link]