CompuCell 3D Modeling environment and pde solver
Download

CompuCell 3D Ranking & Summary

CompuCell 3D Tags

simulate simulation pde solver Modeling environment cellular simulation cellular

CompuCell 3D Description

Modeling environment and pde solver CompuCell 3D is an open source modeling environment and pde solver, primarly used to study cellular behavior. CompuCell 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. The code is built on C++ with a Python wrapper. Users can easily define model parameters in an XML file and run the simulation with our GUI, the CompuCell Player. CompuCell 3D offers an easy interface to complex models as well as real time visualization of their simulations. Requirements: · Python 2.5 or later What's New in This Release: · New, redesigned CompuCell Player featuring steering capabilities, ability to · replay previously saved simulation results, better graphics rendering using VTK · and many other improvements. Introduced ability to add new types of user- · defined and user-controlled fields which can be rendered in the new player. · For MacOS we distribute small, but useful application written by David Larson · that allows users to pixelize experimental pictures and convert them into PIF · initialization files. Users simply "paint" the experimental image and assign cell · types to the painted regions. · Added experimental , external modules that solve subcellular networks models · written in SBML. This feature is still in the beta version but seems to integrate · with CC3D very well. We will update users on our progress in this respect. · Ability to run simulations in a silent mode (not using Player). The results are · stored in the VTK format and can be post-processed using either CompuCell · Player or custom written scripts. · Renamed Plasticity to Elasticity. All simulations written for CC3D version · previous to current and using Plasticity plugins should be updated and change · word "Plasticity" to "Elasticity". This naming convention corresponds better to · what these plugins implement. · Restructured source code directory structure · New reaction-diffusion solver which allows users to specify custom terms and · does not require recompilation · Updated functionality for Elasticity plugins, ContactLocalProduct plugin, · Numerous bug fixes

CompuCell 3D Related Software