A MATLAB toolbox for the exact calculation of stationary states + parameter sensitivity analysis & fitting of stochastic logical models. The toolbox is the accompanying tool to this publication where the mathematical method behind it is described.
Author: Mihály Koltai, Computational Systems Biology of Cancer group at Institut Curie.
Read the tutorial here.
- export_fig (export figures as EPS/PDF/PNG as they appear on screen)
- Customizable heatmaps (for heatmaps)
- Redblue colormap (for heatmaps)
- distinguishable_colors (for lineplots of one dimensional parameter scans. Requires Image Processing toolbox!)
- tight subplots (for customizable gaps between subplots)
- Simulated annealing (parameter fitting by simulated annealing)
These libraries are for visualizations and parameter fitting, not for the calculations themselves, so they are optional, but we recommend using them for all the features of the toolbox.
For the detailed examples of calculations read the tutorial here.