The NEURON simulation environment
Neural Computation
Shapes in the shadow: evolutionary dynamics of morphogenesis
Artificial Life
Modern C++ design: generic programming and design patterns applied
Modern C++ design: generic programming and design patterns applied
Design patterns explained: a new perspective on object-oriented design
Design patterns explained: a new perspective on object-oriented design
Patterns in Scientific Software: An Introduction
Computing in Science and Engineering
Multi-model simulations of chicken limb morphogenesis
ICCS'03 Proceedings of the 2003 international conference on Computational science: PartIII
Problem-Solving Environments for Biological Morphogenesis
Computing in Science and Engineering
From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development
Computing in Science and Engineering
Mathematical analysis of branching morphogenesis
COMPUCHEM'08 Proceedings of the 2nd WSEAS international conference on Computational chemistry
A computational system for investigating chemotaxis-based cell aggregation
ECAL'07 Proceedings of the 9th European conference on Advances in artificial life
Technical Section: Developmental modelling with SDS
Computers and Graphics
A robust in silico analogue of MDCK cystogenesis mimics growth in multiple culture conditions
Proceedings of the 2011 Workshop on Agent-Directed Simulation
A Mathematical Model to Study the Dynamics of Epithelial Cellular Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Multiagent and Grid Systems
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We present CompuCell3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. CompuCell3D employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. CompuCell3D uses design patterns for speed, efficient memory management, extensibility, and flexibility to allow an almost unlimited variety of simulations. We have verified CompuCell3D by building a model of growth and skeletal pattern formation in the avian (chicken) limb bud. Binaries and source code are available, along with documentation and input files for sample simulations, at http://compucell.sourceforge.net.