scripts to build 1D and 2D bifurcation diagrams

./1D_bifurcation_diagrams/1D_BD.ipynb - jupyter notebook that builds 1D bifurcation diagrams

./RhoA_Rac1_phenom_model.bngl - bngl file of the model. Please note, that although model structure corresponds to Eq. 6, the parameters in this file are given just for example, they are not equal to the actual model parameters.

./multicorePC_seq.sh - script to run DIVYPAC software (https://bitbucket.org/andreadega/dyvipac-python/src/master/)
This script starts DYVIPAC python package to run sampling of parameter space and determine number of steady states and their type. Paths to SBML model file and constraints file must be specified in the script. The script must be located in the same folder as run_seq.sh file of DYVIPAC package. Example of run (see DYVIPAC documentation for details):
./multicorePC_seq.sh CORES RUNS SAMPLERUNS PARAMSFILE
Where:
 - CORES is a number of cores for parallel run
 - RUNS and SAMPLERUNS specify number of points to be sampled, total number of sampled points is RUNS*SAMPLERUNS (see DYVIPAC documentation for details)
 - PARAMSFILE is a path to the file with parameters to be sampled (see DYVIPAC documentation for details)
 
 ./2D_bifurcation_diagrams - example folder with input and output files of DIVYPAC, this example illustrates calculation of 2D bifurcation diagram presented in Figs. 2A and S2A.
 ./2D_bifurcation_diagrams/RhoA_Rac1_phenom_model_sbml.xml - sbml model file with correct parameters
 ./2D_bifurcation_diagrams/RhoA_Rac1_phenom_model_params.txt - file with parameters to be sampled
 ./2D_bifurcation_diagrams/RhoA_Rac1_phenom_model_constr.txt - file of model constraints
 ./2D_bifurcation_diagrams/20190514_2135_outputCores4RhoA_Rac1_phenom_model_params.txt.txt - output of DYVIPAC
 ./2D_bifurcation_diagrams/20190514_2135_outputCores4RhoA_Rac1_phenom_model_params.txt.txt_* - unnecessary output files of DYVIPAC
 After running of multicorePC_seq.sh is finished, the output file must be renamed to "output.txt", and then convert_to_numbers.py python script must be run. This script will generate output_numbers.txt file which serves as an input for scan_contour_plot.py python script which plots the first draft of 2D bifurcation diagram. Then this draft must be manually edited to reach the desired level of formatting.
./2D_bifurcation_diagrams/2D_scan.png - example of output of scan_contour_plot.py python script
./2D_bifurcation_diagrams/nullclines and ./2D_bifurcation_diagrams/nullclines_zoom_in - folders with scripts for plotting nullclines and time courses for desired points in parameter space.
