tme-bistability

Copyright (c) 2025 by the authors. All rights reserved.

Citation

If you use this code or parts of it, please cite the following references:

Ryu, H., Röblitz S., Larripa, K. and Frank, A. S. (2025). Modeling Bistable Dynamics Arising from Macrophage–Tumor Interactions in the Tumor Microenvironment. bioRXiv preprint. doi: https://doi.org/10.1101/2025.06.24.661275.

See LICENSE for more details

Questions or support contact:

• Anna-Simone Frank (email: asfrank88@gmail.com)

Download the code

You can download the code at: https://github.com/a-sfrank/tme-bistability.git

General Information

The code studies bistable dynamics in macrophage–tumor interactions within the tumor microenvironment. It solves a system of ODEs, calculates steady states and their stability. In addition, it determines the basin of attractions and produces bifurcation diagrams.

The code generates the results presented in the article:

Ryu, H., Röblitz S., Larripa, K. and Frank, A. S. (2025). Modeling Bistable Dynamics Arising from Macrophage–Tumor Interactions in the Tumor Microenvironment. bioRXiv preprint. doi: https://doi.org/10.1101/2025.06.24.661275.

Included Code Files and Descriptions

Folders:

1. Basin_of_Attraction folder contains following files:

• parameters.m: Parameter file with baseline parameter values and specific cases.
• population_model_v2.m [Main run file]: Files solves ODE system, determines steady states and calculates stability. It also plots time-series of dynamics.
• Jacobian_Sym_population_model: Files symbolically calculates the Jacobian matrix of the ODE system, which is needed for stability analysis.
• Basin_of_attraction [Main run file]: File calculates the Basin of attractions and takes as input the steady states determined from population_model_v2.m. You are prompted to specify the parameter case.

2. Bifurcation_stability_analysis folder contains the following files:

• parameters.m: Parameter file with baseline parameter values and specific cases.
• odefun: Specifies the ODE equations with adaptations to bifrucation analysis.
• Bifurcation_Analysis_ODE23s.m [Main run file]: Files calculates the bifurcation plots for different bifurcation parameters, tumor inital conditions and parameter cases. This information has to be specified within the file before running it.

Output:

• Results are mainly figures which are saved to Figures/-folders.

How to Run the Code

• Open one of the [Main run files]:
  • For population_model_v2.m you are promoted to specify which parameter case to run.
  • For Basin_of_attraction you are prompted to specify which plot you want, e.g., M0 vs T or M2 vs T. By default it always runs parameter case: Case = 2.
  • For Bifurcation_Analysis_ODE23s.m specify specific parameters within the file before running manually.

For additional details, check the artcile or contact the authors.