Systems biology of ferroptosis: a modeling approach (source code)
Description
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 (konstorum@uchc.edu) 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)