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Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes.
Please check our new repository: https://github.com/CNS-OIST/STEPS
An application create, simulate and adjust N-linked glycosylation.
... is used to adjust the kinetic parameters of Michaelis-Menten equations in glycosylation reaction network. A dynamic plot is supplied to show the value of mole amout and mole fraction of various glycoform.
Thanks to Alexey Balakin and Alessandro Presta. Alexey Balakin supply mathgl(https://sourceforge.net/projects/mathgl) that make the implementation of dynamic plot in this application easily. Alessandro Presta supply fga(https://sourceforge.net/projects/fga) that provide a powerful use of GA.
CheMecher is a fully-featured chemical simulator that supports an arbitrary number of reaction steps and chemical species. Uses the Runge-Kutta algorithm for numeric solutions.
The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network.
Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!
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4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
Trelis is a graphical Monte Carlo simulation tool for modeling the time evolution of chemical reaction systems involving small numbers of reactant molecules, such as occur in subcellular biological processes like genetic regulatory networks.
Extensible 3-dimensional chemical reaction modeling tool that utilizes the known scientific rules and theorems to predict complex molecular reactions on an organismal level. Will serve as a starting point for developing a simulated organism.