Systems biology of ferroptosis: a modeling approach (source code)

Source code to reproduce figures in

A. Konstorum, L. Tesfay and B.T. Paul et al., Systems biology of ferroptosis: a modeling approach, Journal of Theoretical Biology, https://doi.org/10.1016/j.jtbi.2020.110222

Software necessary for the code: Matlab

Contact: Anna Konstorum ([e-mail])

Instructions to reproduce select figures (code below can be modified to reproduce the remaining simulation figures):

Figure 2:
Panel (a)
>>Ferroptosis_model(40,2,0,0);

Panel (b)
+ Erastin: >>Ferroptosis_model(40,2,2,0);
+ RSL3: >>Ferroptosis_model(40,2,0,2);

Figure 3:
Panel (a) >>Ferroptosis_model(40,0,0,0);
Panel (b) >>Ferroptosis_model(40,0,0,2);

Figure 6:
Require: Ferroptosis_model_index.m to run Ferop_index_full.m
>>[Ferrop_Index_Base,Ferrop_Index_Erastin] = Ferrop_index_full(40);

Test varying initial conditions (see Supplementary Information, S1)
If base_var=erastin_var=0, then 1000 different runs of the simulations
with varying initial conditions result in the same steady state
Require: Ferroptosis_model_IC.m to run Ferrop_IC.m
>>[base_var,erastin_var] = Ferrop_IC(1000)

源代码，用于重现《A. Konstorum, L. Tesfay 和 B.T. Paul 等人，铁死亡系统生物学：一种建模方法，理论生物学杂志，https://doi.org/10.1016/j.jtbi.2020.110222》中所述的图示。

所需软件：Matlab

联系方式：Anna Konstorum ([e-mail])

重现选定图示的指令（以下代码可修改以重现剩余的仿真图示）:

图2：

面板(a)
>>Ferroptosis_model(40,2,0,0);

面板(b)
+ Erastin: >>Ferroptosis_model(40,2,2,0);
+ RSL3: >>Ferroptosis_model(40,2,0,2);

图3：

面板(a) >>Ferroptosis_model(40,0,0,0);
面板(b) >>Ferroptosis_model(40,0,0,2);

图6：

要求：运行 Ferop_index_full.m 需要提供 Ferroptosis_model_index.m
>>[Ferrop_Index_Base,Ferrop_Index_Erastin] = Ferrop_index_full(40);

测试不同的初始条件（参见补充信息，S1）。若 base_var=erastin_var=0，则1000次不同初始条件的仿真运行将导致相同的稳态。

要求：运行 Ferrop_IC.m 需要提供 Ferroptosis_model_IC.m
>>[base_var,erastin_var] = Ferrop_IC(1000)。