Stochastic Bifurcation Analyser
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CME
Elementary
Examples
FokkerPlanck Update Aug 31, 2014
ParametricAnalysis
Solvers
README.md

README.md

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StoBifAn/TPA

Stochastic Bifurcation Analyser & Tensor-structured Parametric Analysis

The StoBifAn toolbox aims for automated, efficient analysis of high-dimensional well-mixed stochastic biochemical systems.

Feature highlights:

  • 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.

Read more

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.

Related

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.

Lisence

Creative Commons License
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.