HHIP's Dynamic Role in Epithelial Wound Healing Reveals a Potential Mechanism of COPD Susceptibility - Supporting files of the expanded Boolean model (shown on Figure 4)

This is a collection of files necessary to reproduce a subset of the results discussed in the manuscript entilted HHIP’s Dynamic Role in Epithelial Wound Healing Reveals a Potential Mechanism of COPD Susceptibility by Deritei et al. (accepted for publication at PNAS).

Files are read by the dynmod software (https://github.com/Ravasz-Regan-Group/dynmod) to simulate the largeer Boolean model’s (shown on Fig. 4 and Supplemental Fig S2) behaviors. These include the model in .dmms format (as well as .BooleanNet and .SBML formats, namely COPD_EMT_CellCycle_Apoptosis.dmms, COPD_EMT_CellCycle_Apoptosis_Fine.booleannet, the “in silico protocol” files for reproducing all figures (COPD_Figures.vex), re-running the validation experiments (Validation_Table_COPD_EMT_CellCycle_Apoptosis.vex) and running a python script that performs all validation statistical tests and generating a results list (Large Model Validation Script.py, ST5 - Large model validation.csv).

The _EXP folder contains exported figures necessary for generating the main manuscript Figure 5 and Supplemental Figures 3-7.