CompuCell3D

Category Cross-Omics>Agent-Based Modeling/Simulation/Tools

Abstract CompuCell3D is an open source modeling environment and partial differential equation (PDE) solver, primarily used to study 'cellular behavior'.

CompuCell3D was initially developed to help researchers (biologists and physicists) model materials and tissues without having to dedicate resources to developing code that will reproduce existing software.

CPM - Foundations for Tissue --

CompuCell3D is based on the Cellular Potts Model (CPM).

While the Potts model was originally developed to study ferromagnetic and crystalline systems; in the late 80's and 90's, Francois Graner and James Glazier extended the Potts model to study the coarsening of foam and sorting of biological cells.

Since then modelers have continued to use the CPM to study foam, morphogenesis, biofilms, cancer, as well as many other biological and physical systems.

CompuCell3D developed as a framework --

The manufacturer developed CompuCell3D as a framework for Glazier- Graner-Hogeweg (GGH) model aka Cellular Potts Model (CPM) simulations.

Unlike specialized research code, CompuCell3D is a 'simulation environment' that allows researchers to rapidly build and run shareable GGH-based simulations.

It greatly reduces the need to develop custom code and its adherence to open-source standards ensures that any such code is shareable.

CompuCell3D supports non-programmers by providing visualization tools, an eXtensible Markup Language (XML) interface for defining simulations, and the ability to extend the framework through specialized modules.

The C++ computational kernel of CompuCell3D is also accessible using the open-source scripting language Python, allowing users to create complex simulations without programming in lower-level languages such as C or C++.

Unlike typical research code, changing a simulation does Not require recompiling CompuCell3D.

Users define simulations using CompuCell3D XML (CC3DML) configuration files and/or Python scripts.

CompuCell3D reads and parses the CC3DML configuration file and uses it to define the basic simulation structure, then initializes appropriate Python services (if they are specified) and finally executes the underlying simulation algorithm.

CompuCell3D is modular: each module carries out a defined task.

CompuCell3D terminology calls modules associated with index copies or index-copy attempts 'plug-ins'.

Some plug-ins calculate changes in effective energy, while others (lattice monitors) react to accepted index copies, e.g., by updating generalized cells’ surface areas, volumes or lists of neighbors.

Plug-ins may depend on other plug-ins. For example, the Volume plug- in (which calculates the volume-energy constraint) depends on VolumeTracker (a lattice monitor), which, as its name suggests, tracks changes in generalized cells’ volumes.

When implicit plug-in dependencies exist, CompuCell3D 'automatically loads' and initializes dependent plug-ins.

In addition to plug-ins, CompuCell3D defines modules called 'steppables' which run either repeatedly after a defined intervals of 'Monte Carlo Steps' or once at the beginning or end of the simulation.

Steppables typically define initial conditions, alter cell states, update fields or output intermediate results.

CompuCell3D includes a Graphical User Interface (GUI) and visualization tool, 'CompuCell Player' (also referred to as Player).

From Player the user opens a CC3DML configuration file and/or Python file and hits the “Play” button to run the simulation.

Player allows users to define multiple 2D or 3D visualizations of generalized cells, fields or various vector plots while the simulation is running and save them automatically for post-processing.

Integration with SBW --

The manufacturer has conducted a preliminary integration of CompuCell3D with the Systems Biology Workbench (SBW) (see G6G Abstract Number 20453) to link to Subcellular models.

As a result users can select the level of detail in their models while working within a single integrated framework.

System Requirements

Contact manufacturer.

Manufacturer

CompuCell3D was created in collaboration between groups at IU and Notre Dame.

Manufacturer Web Site CompuCell3D

Price Open source.

G6G Abstract Number 20452

G6G Manufacturer Number 104079