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.

MOTIVATION: CompuCell is a multi-model software framework for simulation of the development of multicellular organisms known as morphogenesis. It models the interaction of the gene regulatory network with generic cellular mechanisms, such as cell adhesion, division, haptotaxis and chemotaxis. A combination of a state automaton with stochastic local rules and a set of differential equations, including subcellular ordinary differential equations and extracellular reaction-diffusion partial differential equations, model gene regulation. This automaton in turn controls the differentiation of the cells, and cell-cell and cell-extracellular matrix interactions that give rise to cell rearrangements and pattern formation, e.g. mesenchymal condensation. The cellular Potts model, a stochastic model that accurately reproduces cell movement and rearrangement, models cell dynamics. All these models couple in a controllable way, resulting in a powerful and flexible computational environment for morphogenesis, which allows for simultaneous incorporation of growth and spatial patterning. RESULTS: We use CompuCell to simulate the formation of the skeletal architecture in the avian limb bud. AVAILABILITY: Binaries and source code for Microsoft Windows, Linux and Solaris are available for download from http://sourceforge.net/projects/compucell/

ProtoMol is a high-performance framework in C++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates that enable generation of efficient code for sections critical to performance (generic programming). The framework encapsulates important optimizations that can be used by developers, such as parallelism in the force computation. Its design is based on domain analysis of numerical integrators for molecular dynamics (MD) and of fast solvers for the force computation, particularly due to electrostatic interactions. Several new and efficient algorithms are implemented in ProtoMol. Finally, it is shown that ProtoMol's sequential performance is excellent when compared to a leading MD program, and that it scales well for moderate number of processors. Binaries and source codes for Windows, Linux, Solaris, IRIX, HP-UX, and AIX platforms are available under open source license at http://protomol.sourceforge.net.