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is a interactive molecular visualisation program designed especially designed for coarse-grained simulation of non-spherical particles. Ellipsoids (Gay-Berne), disks, and custom shaped uniaxial particle (e.g. pear-shaped particles) can be represented.
QMGA is a Qt-based molecular graphics application for visualizing large ensembles of ellipsoids, spherocylinders or spheres. It is conceived for coarse-grained mesoscopic molecular simulation, but can be used for any kind of convex body systems.
A novel stochastic simulation environment for biochemical modeling
UPDATE(2017-07-24) This repository has moved to BitBucket: https://bitbucket.org/parkinsonlab/cell-2017
Cell++ is a novel stochastic simulation environment which is capable of modeling diverse biochemical phenomena including signal transduction pathways, metabolic pathways and intracellular calcium signaling.