Stochastic Bifurcation Analyser & Tensor-structured Parametric Analysis
The StoBifAn toolbox aims for automated, efficient analysis of high-dimensional well-mixed stochastic biochemical systems.
- Assemble the large dimensional chemical master equation (CME) and the chemical Fokker-Planck equation (CFPE) in the low-parametric, separable, and rank-structured tensor format.
- Solve for the steady state distributions from the CMEs/CFPEs simultaneously for ranges of multiple parameter values.
- Study the identifiability of model parameters based on the Method of Moments (MOM), and estimate the parameter values.
- Directly compute the bifurcation structure of the large dimensional stochastic reacting systems.
- Couple the intrinsic and extrinsic noise into the steady state computation, the so-called robustness analysis.
- Sensitivity analysis of the parametric stationary distributions.
For more information regarding the methodologies, please refer to:
Liao, S., Vejchodsky, T. & Erban, R. (2014). Parameter estimation and bifurcation analysis of stochastic models of gene regulatory networks: tensor-structured methods. arXiv preprint arXiv:1406.7825.
The MATLAB files are built upon the TT-Toolbox.
Note: We are still commenting and uploading parts of the coding templates. You are welcome to contact liao@maths.ox.ac.uk, for any questions about StoBifAn.
StoBifAn by Shuohao Liao is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Based on a work at https://github.com/Jackyhaorockman/StoBifAn.
