Protrusion force cooperate with cell-cell adhesion-induced local cell polarity alignment to regulate switching between radial and directional collective tumor migration

This is code repository for the paper: Protrusion force cooperate with cell-cell adhesion-induced local cell polarity alignment to regulate switching between radial and directional collective tumor migration.

Folders

s1_model: Folder containing CompuCell3D models.

• 12222021_force_fpp_single: CompuCell3D model for simulating microtumor dynamics.

• 12222021_force_fpp_scan: CompuCell3D model parameter scans.

s2_model_simulation: Folder containing code for submitting simulation jobs to the cluster.

s3_model_analysis: Including microtumor migration mode clustering model and code for geometric analysis.

• 01_geo_feature_calc.ipynb: microtumor geometric feature calculations.

• 02_two_step_clustering.ipynb: microtumor migratory mode clustering.

• clustering_models: folder containing saved clustering models.

• 20250129-msmm-model-analysis: folder containing clustering results for simulation results.

s4_figures: Folder containing code for generating figures in the paper. Code for generating figure 1, 3, 4, 5 are archived in individual folders.

• Figure1: Folder containing code showing enriched GO terms

• Figure3: Folder containing code for Figure 3.

  • 20221201_Figure3_props_polarity.ipynb: calculate example tumor properties and polarity at the final time point.

  • 20250203_Figure3_scan_props.ipynb：Plot microtumor emergent properties for parameter scan.

  • 20221201_Figure3_h.ipynb: Plot microtumor migratory mode distribution in emergent properties space.

  • Directional: folder containing simulation results for a directionally migratory tumor

  • Radial: folder containing simulation results for a radially migratory tumor

  • Results: folder containing generated figures.

• Figure4_n_5: Folder containing code generating Figure 4 and 5.

  • 20220329_Figure4_a.ipynb: Plot migratory mode percentage in selected parameter range

  • 20220602_Figure4_cd.ipynb: Plot selected tumor migratory properties

  • 20220426_Figure5_e.ipynb: Plot migratory mode percentage in selected parameter range

  • 20221105_Figure5_ij.ipynb: Plot selected tumor migratory properties

  • myosin_selected: folder containing selected simulation results for migratory tumor with and without myosin inhibition

  • akt2_selected: folder containing selected simulation results for migratory tumor with and without AKT2 inhibition

s5_supplements: Folder containing model, data and code for supplemental simulations, where we scanned coupling strength beta as free parameter. beta values simulated are 0, 0.3,0.6,1

• 20250128_simulation_scan_betas.ipynb: Code for submitting simulation jobs to cluster

• 20250131_analysis_1_geo_feature_calc_beta_scans.ipynb: Code for tumor geometric feature analysis

• 20250203-analysis-2-two-step-clustering-beta-scans.ipynb: Code for clustering tumor migration code using previous trained clustering model

• 20250203_analysis_3_plots_beta_scans.ipynb: Code for plotting the emergent properties for microtumors

• 20250129-update-msmm-model: Folder containing CompuCell3D models for scanning beta values

• 20250129-update-msmm-model-analysis: Folder containing clustering results for simulations.

src: Folder containing code modules that are frequently used in this paper.