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Python Scripting Manual for CompuCell3D - version 3.7.8

The focus of this manual is to teach you how to use Python 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.

.. toctree::
   :maxdepth: 2

   introduction
   how_to_use_python_in_cc3d
   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
   parameter_scans
   restarting_simulations
   implementing_energy_functions_in_python
   appendix_a
   appendix_b