Use scripts in ligands_free folder to simulate the model, create data and plot the results used in the manuscript.
- simulations for different test conditions:
use
1- 01_different_IC_different_FC_ligands_free.py for ligand competition different initial conditions
2- 02_equal_IC_different_FC_ligands_free.py for ligand competition equal initial conditions
3- 03_equal_IC_equal_FC_ligands_free.py for ligand competition equal initial conditions, equal fold change
4- 04_equal_IC_high_FC_ligands_free.py for ligand competition equal intial condition, high fold change for L2
5- 05_different_IC_equal_BR_ligands_free.py for ligand competition equal initial conditions, equal binding rates
all these scripts export the simulation results in csv files.
read these files in:
06_plots_simulations.R to plot the results.
-
parameter scan of L2 initial condition (manual)
use
07_paramScan_manual_L2.py to do the parameter scan for L2=0.5 to L2=2.97
exports to csv
then use
06_plots_simulations.R to plot the results. -
Parameter Sensitivity analysis of the original ligand competition model with excess ligands compared to integrins:
use
08_parameterSensitivity_calculations.py
then use
09_parameterSensitivity_formula_plot.R to plot. -
Parameter Sensitivity of the ligand competition model with excess integrins compared to ligands:
use
10_parameterSensitivity_calculations_integrin_excess.py
then the script below plots the supplementary figure 2
11_parameterSensitivity_formula_plot_integrins_excess.R -
extras:
12_no_competition.py : simulates the model without competition
equations.ipynb : prints out the differential equations of the model
simulation_results_data : folder that contains all the raw data from simulations at each test condition, same numbering 1-5 is used for test conditions is used here
ligandCompetitionModel.sbml : SBML file for the ligand competition model, use this and the initial concentrations given in Table 1 of the publication to reproduce the results