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Spatial stochastic simulation

Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic…
MEANS
Desktop

MEANS Moment Expansion Approximation iNference and Simulation

Implements an efficient moment expansion approximation with parametric closures…

Implements an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment. MEANS enables the analysis of complex stochastic systems…

StochPy
Desktop

StochPy Stochastic modeling in Python

Provides a stochastic dynamics simulator. StochPy supplies various stochastic…

Provides a stochastic dynamics simulator. StochPy supplies various stochastic simulation algorithms (SSAs) for the simulation of stochastic and supports model definition with added statistical…

SELANSI
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SELANSI SEmi-LAgrangian SImulation of GRNs

Approximates the chemical master equation (CME) by the partial integral…

Approximates the chemical master equation (CME) by the partial integral differential equation (PIDE) model. SELANSI is a toolbox for simulation of stochastic multidimensional gene regulatory…

StochKit
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StochKit

Provides methodology for running stochastic simulations. StochKit contains an…

Provides methodology for running stochastic simulations. StochKit contains an algorithm that selects the step size based on an error tolerance and reverts to the stochastic simulation algorithm (SSA)…

SMeagol
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SMeagol

Generates highly realistic single molecule microscopy time-lapse image series…

Generates highly realistic single molecule microscopy time-lapse image series aimed primarily at single particle tracking applications. The purpose of SMeagol is to enable realistic comparisons…

MesoRD
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MesoRD

A tool for simulating stochastic reaction-diffusion systems as modeled by the…

A tool for simulating stochastic reaction-diffusion systems as modeled by the reaction diffusion master equation. The simulated systems are defined in the Systems Biology Markup Language with…

IMP
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IMP Integrative Modeling Platform

A package which facilitates the writing of integrative modeling applications,…

A package which facilitates the writing of integrative modeling applications, the development of new model representations, scoring functions, sampling schemes, and analysis methods, and the…

LASSIE
Desktop

LASSIE LArge-Scale SImulator

Simulates large-scale reaction-based models of cellular processes. LASSIE…

Simulates large-scale reaction-based models of cellular processes. LASSIE automatically converts reaction-based models of biological systems into the corresponding systems of Ordinary Differential…

FERN
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FERN Framework for the Evaluation of chemical Reaction Networks

Serves for stochastic simulation and analysis of chemical reaction networks.…

Serves for stochastic simulation and analysis of chemical reaction networks. FERN is a Java framework for modeling and simulating biological systems which provides accurate and state-of-the-art…

SmartCell
Desktop

SmartCell

Aims users to manage cell geometry, and allows localisation of species.…

Aims users to manage cell geometry, and allows localisation of species. SmartCell provides a method to model biological processes. This method combines a stochastic approximation with diffusion and…

Bio-SPICE
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Bio-SPICE

Allows users to model and simulate spatio-temporal processes in living cells.…

Allows users to model and simulate spatio-temporal processes in living cells. Bio-SPICE is a framework and software toolkit that consists of (i) the Dashboard, (ii) data analysis tools, (iii)…

GridCell
Desktop

GridCell

A three-dimensional simulation environment for investigating the behaviour of…

A three-dimensional simulation environment for investigating the behaviour of biochemical networks under a variety of spatial influences including crowding, recruitment and localization. GridCell…

URDME
Desktop

URDME

A modular software framework for spatial stochastic simulation. The goal of…

A modular software framework for spatial stochastic simulation. The goal of URDME is twofold: firstly, it provides applied users with a powerful and user-friendly modeling environment that supports…

STEPS
Desktop

STEPS STochastic Engine for Pathway Simulation

A package for exact stochastic simulation of reaction-diffusion systems in…

A package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries. Our core simulation algorithm is an implementation of Gillespie's SSA, extended to…

xCellerator
Desktop

xCellerator

Allows user to analyze biochemical networks. xCellerator is useful for…

Allows user to analyze biochemical networks. xCellerator is useful for deterministic simulations in Mathematica.

permute
Desktop

permute

Provides a method to make split-plot designs. permute allows users to exchange…

Provides a method to make split-plot designs. permute allows users to exchange whole-plots or split-plots in these designs.

CellMC
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CellMC

Generates a program that implements stochastic simulation algorithm (SSA) for a…

Generates a program that implements stochastic simulation algorithm (SSA) for a model expressed as SBML. CellMC is an open source program generator that compiles a mesoscopic model of a biochemical…

ProMesh
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ProMesh

Provides support for unstructured grids of 1, 2, and 3 dimensions. ProMesh is a…

Provides support for unstructured grids of 1, 2, and 3 dimensions. ProMesh is a flexible cross-platform meshing software which features a broad range of modular tools to generate, remesh, transform,…

MeshLab
Desktop

MeshLab

Processes and edits unstructured large 3D triangular meshes. MeshLab is a…

Processes and edits unstructured large 3D triangular meshes. MeshLab is a system aimed to help the processing of the typical not-so-small unstructured models arising in 3D scanning. The software…

Cyto-Sim
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Cyto-Sim

Consists in a stochastic simulator. Cyto-Sim allows user to represent different…

Consists in a stochastic simulator. Cyto-Sim allows user to represent different types of cells which communicate via ligands and receptors. With this tool, membranes can be used to model notional…

BioSpreadsheet
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BioSpreadsheet

Allows edition of System Biology Markup Language (SBML) models.

Allows edition of System Biology Markup Language (SBML) models.

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