About: The files in this repository constitute a multi-approach and multi-scale model of CD4+ T lymphocytes.
Execution: Running the main.m file within the MATLAB environment will start a stochastic simulation of CD4+ T cells responding to the input signals defined in antigen.mat. Note that all the files in the repository must be placed in the same directory as the main.m file during a simulation.
Copyright: Helikar Lab, University of Nebraska–Lincoln.
Licence: GNU General Public License v3.0.
Software requirements:
- MATLAB R2020a.
- The Cobra (COnstraint-Based Reconstruction and Analysis) Toolbox is needed to optimise the metabolic fluxes. It is available at https://opencobra.github.io/cobratoolbox/stable/.
Inputs: Within antigen.mat, the user must provide an input signal representing the temporal trajectory of the abundance of pathogens/antigens in each compartment.
Configuration of the main.m file to parameterise the model to describe the problem under consideration:
- Set up the compartments by providing Qa, Qb, Vt, Vln, and Vc on lines 99 to 103.
- Specify the initial number of agents in each compartment and the number of CD4+ T cells in the body part corresponding to that compartment: Nt0, Nln0, Nc0, Nt0_all, Nln0_all, and Nc0_all on lines 77 to 82.
- Specify the initial cytokine concentrations in the compartments: IL20, IL40, IL60, IL120, IL170, IL180, IL210, IL230, IL270, IFNg0, and TGFb0 on lines 119 to 129.
- Specify the cytokine production rates associated with the inputs: PIL2in, PIL4in, PIL6in, PIL12in, PIL17in, PIL18in, PIL21in, PIL23in, PIL27in, PIFNgin, and PTGFbin on lines 106 to 116.
- Specify the extent and grain of the simulation by providing the number of time steps (steps on line 48) and the step size (step_size on line 49).
- Specify the number of times the model must be implemented to achieve robust average results: rounds on line 52. This should be decided by a convergence study.
- Fix the four calibration parameters in relation to the problem under consideration and any experimental data available for calibration: Ease_restim, Ease_ACAD, Ease_memory, and Ease_relax on lines 89 to 92.