CC3D Reference Manual

Introduction

  • Introduction

Intro to CC3D Python Programming

  • Python Tutorials Section

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
  • Search

© Copyright 2024, Maciej H. Swat, Julio Belmonte, T.J. Sego, Pete Fyffe, James A. Glazier.

Built with Sphinx using a theme provided by Read the Docs.