CC3D Reference Manual

Introduction

  • Introduction

Intro to CC3D Python Programming

  • Python Tutorials Section
    • Create Your First CompuCell3D Project
    • Running and Debugging CC3D Simulations Using PyCharm
    • What is a Steppable? (SteppableBasePy class)
    • Adding Steppable to Simulation using Twedit++
    • Iterating over cell neighbors
    • Passing information between steppables
    • How to Check if Two Cells are Unique
    • 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
    • How to Detect Contact
    • Examples: Mitosis
    • Custom Cell Attributes in Python
    • Adding and managing extra fields for visualization purposes
    • Automatic Tracking of Cells’ Attributes

Writing Simulations in Pure Python

  • How to programmatically control every aspect of the simulation

CC3D - How To

  • Common CC3D Tasks
  • Building a wall (it is going to be terrific. Believe me)
  • How to Check if Two Cells are Unique
  • Examples: Mitosis
  • Example: Contact-Inhibited Cell Growth
  • Volume and Cell Growth
  • Surface and Cell Contact
  • Mitosis
  • Cell Death
  • Secretion Plugin Reference
  • Field Secretion | Interacting with PDE Solver Fields
  • Chemotaxis on a cell-by-cell basis
  • Steering – changing CC3DML parameters on-the-fly.
  • Steering – changing Python parameters using Graphical User Interface.
  • Replacing CC3DML with equivalent Python syntax
  • Cell Motility. Applying force to cells.
  • Setting cell membrane fluctuation ona cell-by-cell basis
  • Dividing Clusters (aka compartmental cells)
  • Changing cluster id of a cell.

Network Solvers

  • SBML Solver
  • Building SBML models using Tellurium
  • Building SBML models efficiently with Antimony and CellML
  • Building and Using MaBoSS Models

Real-world Examples

  • Real-World Examples Section

Screenshots, Restarts, Parameter Scans

  • Configuring Multiple Screenshots
  • Custom Simulation Visualization Settings
  • Parameter Scans
  • Restarting Simulations

XML Steppables

  • Steppable Section

XML Plugins

  • Plugins Section

XML Expression Evaluator

  • XML Expression Evaluator - muParser

PDESolvers in CompuCell3D

  • Diffusion (PDE Solvers) in CompuCell3D

Intro to Cellular Potts Model

  • Potts and Lattice Section
  • Algorithms & How They Work Section

Legacy Content

  • Transitioning from CC3D 3.x to CC3D 4.x
  • Secretion Plugin (legacy version for pre-v3.5.0)

Appendix

  • Appendix A: List of Base Steppable Functions
  • Appendix B: List of Cell Attributes
  • Direct Call to CompuCell3D from Python
  • Changing number of Worknodes
  • Authors
  • Funding
  • References
CC3D Reference Manual
  • Python Tutorials Section
  • View page source

Python Tutorials Section

  • Create Your First CompuCell3D Project
  • Running and Debugging CC3D Simulations Using PyCharm
  • What is a Steppable? (SteppableBasePy class)
  • Adding Steppable to Simulation using Twedit++
  • Iterating over cell neighbors
  • Passing information between steppables
  • How to Check if Two Cells are Unique
  • 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
  • How to Detect Contact
  • Examples: Mitosis
  • Custom Cell Attributes in Python
  • Adding and managing extra fields for visualization purposes
  • Automatic Tracking of Cells’ Attributes
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© Copyright 2024, Maciej H. Swat, Julio Belmonte, T.J. Sego, Pete Fyffe, James A. Glazier.

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