bifurcation_analysis

Bifurcation analysis of TGF-β1, THBS1, and FMOD network

Figure S8A and S8C

Fitting our model to the experimental data using Gnuplot (version 5.4), we inferred the model parameters.

Below is our bash command:

cd 001_fitting
gnuplot gscript_fitting_Fig3A.txt
mv 001_fitting/fit.log 001_fitting/fit_gscript_fitting_Fig3A.log

gnuplot gscript_fitting_Fig2AB.txt
mv 001_fitting/fit.log 001_fitting/fit_gscript_fitting_Fig2AB.log

The results are stored in 001_fitting/fit_gscript_fitting_Fig3A.log and 001_fitting/fit_gscript_fitting_Fig2AB.log.

Figures 4B, S8B, and 4D

We computed a bifurcation diagram of [TGFβ1] with respect to parameters for THBS1 and FMOD.

Below is our bash command:

cd 002_control_pq
bash aout_001.sh
bash aout_002.sh
gnuplot gscript_pq.txt

Also, we computed bifurcation diagrams of [THBS1], [FMOD], and [TGFβ1] with respect to a parameter for THBS1 by the following command:

cd 003_control_p_THBS1
bash aout_001.sh
bash aout_002.sh
gnuplot gscript_p.txt

Similarly, we computed bifurcation diagrams of [THBS1], [FMOD], and [TGFβ1] with respect to a parameter for FMOD by the following command:

cd 004_control_q_FMOD
bash aout_001.sh
bash aout_002.sh
gnuplot gscript_q.txt

Likewise, we computed bifurcation diagrams of endogenous [THBS1], [FMOD], and [TGFβ1] with respect to a parameter gamma for TGF-β1 using the following command:

cd 010_control_r_PDL
bash aout_001.sh
bash aout_002.sh
gnuplot gscript_r.txt

Figures 4C and S10B

We computed distributions of [THBS1] and [FMOD] with respect to a parameters for THBS1.

Below is our bash command:

cd 020_stochastic_simulation_forK1
bash aout.sh

Similarly, we computed distributions of [THBS1] and [FMOD] with respect to a parameters for FMOD.

Below is our bash command:

cd 021_stochastic_simulation_forK2
bash aout.sh

Likewise, we computed distributions of endogenous [THBS1] and [FMOD] with respect to a parameter gamma for TGF-β1 using the following command:

cd 030_stochastic_simulation_forGamma
bash aout.sh