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CompuCell3D
Project Overview
Description: We proudly announce third CompuCell3D Training Workshop that will be hosted by Biocomplexity Institute at Indiana University, May 2009. Exact date will be given soon . For more information please visit:

http://www.compucell3d.org/

Modeling the behavior of multi-cell biological systems using multi-scale approach is one of the goals behind CompuCel3D project.
CompuCell3D was originally written to model morphogenesis, the process in embryonic development where cells cluster into patterns which eventually differentiate into organs, muscle or bone. Through integration of multiple mathematical models into a software implementation with easy to use XML based syntax scientists were able to build models within few hours as opposed to weeks when writing source code from scratch. compuCell3D is based on Glazier-graner-Hogeweg model (GGH) also known as the Cellular Potts Model (CPM).The model is capable of capturing key cellular behaviors: cell clustering as well as growth, division, death, intracellular adhesion, and volume and surface area constraints;

In addition researchers may include partial differential equation models for external chemical fields which can model reaction-diffusion, and cell type automata to provide a method for categorizing cells by behavior into types and algorithms for changing cell type.
These models can communicate to establish for example cellular reactions to external chemical fields such as secretion or resorption, and cellular responses such as chemotaxis and haptotaxis. Using scripting language (Python) users may build sophisticated intra-cellular models e.g. reaction-kinetics models, gene pathways etc that determine macroscopic properties of cells. Thus using CompuCell3D one can build truly multi-scale, multi-cell models.

The Graphical User Interface CompuCellPlayer, built upon Qt, interactively visualizes these simulations in three dimensions and also provides the ability to switch to 2D cross sections in each dimension, and also the ability to alternate between chemical fields being visualized. Through this player you can easily pause a simulation to view results and restart again, and also use camera techniques such as zooming, rotating, translating and projecting to more easily view results. The Player uses Qt Threads to enable parallel execution with the CompuCell3D back end. Through the player you can save screenshots of a simulation and for long simulations the Player can be run in silent mode to improve performance, generating images every certain number of steps.

CompuCell3D is an example of Problem Solving Environment (PSE) and has further reaching goals than narrowly specialized research code. In general, the PSE's have multiple requirements. It should be able to run simulations in three dimensions, it should be designed for performance and memory consumption due to the potential for large quantities of cells and superimposed fields, it should be flexible and extensible to allow for the addition of new cell behaviors or at a higher level, new models. Also, users will want to visualize cells and/or fields, check results, run benchmarks, pause the simulation and change parameter values and view results, etc.

We provide all these features in a single package - CompuCell3D. Both source code and binaries are available for Windows, Linux and Mac OS X. For complete download selection please visit
http://www.compucell3d.org


We make both tools available for the Linux and MacOS operating systems.

Purpose/Synopsis: CompuCell3D runs 3D multiscale multi-cell simulations, integrating the GGH model , PDE solvers (reaction-diffusion), and cell type automata (differentiation). CompuCell3D runs in parallel with the CompuCellPlayer visualization engine.

Audience: Biologists, physicists, mathematicians and computational scientists interested in multi-scale simulations of multi-cell systems in three dimensions.

Long Term Goals and Related Uses: Allow users to build, test and run multi-scale, multi-cell models of tissues, organs and organisms using cell-based modeling techniques

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