Dr. Denis Tsygankov (2023)
Integrative Systems Biology Lab
Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University SOM
If you use any part of the scripts in this package, please cite:
Siarhei Hladyshau, Jorik P Stoop, Kosei Kamada, Shuyi Nie, Denis V Tsygankov
Spatiotemporal coordination of Rac1 and Cdc42 at the whole cell level during cell ruffling
doi: https://doi.org/10.3390/cells12121638
crop_frame.m - crop cell mask from a large simulation domain
extapolate_C.m - extrapolate values of concentration (A) along the preimeter of the cell mask (Im)
generate_regular_polyhedron.m - generate a binary mask representing a regular polyhedron
geometry_factor.m - copmute probabilities for a geometry factor
laplacian_DT.m - compute discrete laplacian using 5-point stencil with no-flux boundary conditions
outline_8p.m - compute outline of a binary mask as an 8-connected object
U_matrix.m - supplemental finction for computing laplacian
return_frame_to_canvas.m - transform the cropped simulation domain to the large simulation domain
model1: four-component model of GTPase and inhibitor
model2: four-component model of GTPase and inhibitor with regulation of actin factor by GTPase activation rate
model3: six-component model of Rac1 activity induced by Cdc42 with regulation of actin factor by Rac1 activation rate
model4: six-component model of bidirectionally coupled Rac1 and Cdc42 with regulation of actin factor by Rac1 activation rate
model5: eight-component model of Rac1 and Cdc42 activity induced by the upstream effector with regulation of actin factor by Rac1 activation rate
model6: eight-component model of Rac1 and Cdc42 activity (with feedback from Cdc42 to Rac1) induced by the upstream effector with regulation of actin factor by Rac1 activation rate
run_2D_dynamic_cell_model1.m - main script for running simulation of model1
protrude_extrapolate_model1.m - function for computing protrusion probabilities in model1
retract_reduce_model1.m - function for computing retraction probabilities in model1
run_2D_dynamic_cell_model2.m - main script for running simulation of model2
protrude_extrapolate_diff_model2.m - function for computing protrusion probabilities in model2
retract_reduce_diff_model2.m - function for computing retraction probabilities in model2
run_2D_dynamic_cell_model3.m - main script for running simulation of model3
protrude_extrapolate_diff_model3.m - function for computing protrusion probabilities in model3
retract_reduce_diff_model3.m - function for computing retraction probabilities in model3
run_2D_dynamic_cell_model4.m - main script for running simulation of model4
protrude_extrapolate_diff_model4.m - function for computing protrusion probabilities in model4
retract_reduce_diff_model4.m - function for computing retraction probabilities in model4
run_2D_dynamic_cell_model5.m - main script for running simulation of model5
protrude_extrapolate_diff_model5.m - function for computing protrusion probabilities in model5
retract_reduce_diff_model5.m - function for computing retraction probabilities in model5
run_2D_dynamic_cell_model6.m - main script for running simulation of model6
protrude_extrapolate_diff_model6.m - function for computing protrusion probabilities in model6
retract_reduce_diff_model6.m - function for computing retraction probabilities in model6