The focus of this manual is to teach you how to use Python 2 scripting language to develop complex CompuCell3D simulations. We will assume that you have a working knowledge of Python. You do not have to be a Python guru but you should know how to write simple Python scripts that use functions, classes, dictionaries and lists. You can find decent tutorials online (e.g. Instant Python Hacking, or Instant Python Hacking) or simply purchase a book on introductory Python programming.
authors funding introduction transition_to_cc3d_4 how_to_use_python_in_cc3d debugging_cc3d_simulations_in_PyCharm SteppableBasePy_class adding_steppable_to_simulation_using_twedit++ passing_information_between_steppables creating_and_deleting_cells_cell_type_names calculating_distances_in_CC3D_simulations looping_over_select_cell_types_finding_cell_in_the_inventory writing_data_files_in_the_simulation_output_directory adding_plots_to_the_simulation custom_cell_attributes_in_python adding_and_managing_extra_fields_for_visualization_purposes automatic_tracking_of_cells_attributes field_secretion chemotaxis_on_a_cell-by-cell_basis steering_changing_cc3dml_parameters_on-the-fly steering_changing_python_parameters_using_UI replacing_cc3dml_with_equivalent_python_syntax cell_motility_applying_force_to_cells setting_cell_membrane_fluctuation_ona_cell-by-cell_basis checking_if_two_cell_objects_point_to_different_cells modifying_attributes_of_cellg_object controlling_steppable_call_frequency_stopping_simulation_on_demand_or_increasing_maximum_monte_carlo_step building_a_wall resizing_the_lattice changing_number_of_worknodes iterating_over_cell_neighbors mitosis dividing_clusters changing_cluster_id_of_a_cell sbml_solver building_sbml_models_using_tellurium building_SBML_models_efficiently_with_Antimony_and_CellML configuring_multiple_screenshots parameter_scans restarting_simulations calling_cc3d_directly_from_python implementing_energy_functions_in_python appendix_a appendix_b