Search Results for "stochastic"
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Showing 18 open source projects for "stochastic"
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Nemo
Individual-based forward-time genetics simulation software
Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework. -
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MesoRD is a stochastic and deterministic simulator of coupled chemical reactions and diffusions in space.
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ABC-SysBio implements likelihood free parameter inference and model selection in dynamical systems. It is designed to work with both stochastic and deterministic models written in Systems Biology Markup Language (SBML).
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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
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StochPy - Stochastistic modeling in Python - is an easy-to-use package, which provides several stochastic simulation algorithms and unique analysis techniques, which can be used for stochastic simulations of biochemical systems.
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Virus QSP Modeling
C++ and Python code for simulating RNA virus replication
Stochastic simulation model of poliovirus Sabin-to-Mahoney genetic state transition (C++ code). Models genotypes, virus populations, and quasispecies cloud. Simulates replication error and copy-choice recombination. Various parameters guiding the model are user-specified. Python code post-processes simulation output to produce report files. -
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RSSA
Rejection-based stochastic simulation algorithm (RSSA)
Rejection-based stochastic simulation algorithm (RSSA) is an efficient exact algorithm for doing stochastic simulation of biochemical reaction systems. RSSA improves over state of the art of stochastic simulations by avoiding and collapsing as much the number of propensity updates. -
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Hy3S uses advanced MPI parallelized hybrid stochastic simulation methods to quickly compute the dynamics of biochemical networks with thousands of species/reactions. Many features included (see Home Page). An easy-to-use GUI (Matlab req) is included.
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abc-sde
approximate Bayesian computation for stochastic differential equations
A MATLAB toolbox for approximate Bayesian computation (ABC) in stochastic differential equation models. It performs approximate Bayesian computation for stochastic models having latent dynamics defined by stochastic differential equations (SDEs) and not limited to the "state-space" modelling framework. Both one- and multi-dimensional SDE systems are supported and partially observed systems are easily accommodated. -
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simbTUM
Simulation of stochastic processes and ODE models in biology.
SIMulation of Biological systems (developed at the TU Munich) This program allows to define ODE-models or stochastic compartemental models of biological processes, to simulate, to fit data and to do some statistics (fitting and statistics for deterministic models only). -
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YasimSBML (Yet another simulator for SBML) is a stochastic simulator of metabolic networks in SBML format. Unlike traditional simulators (Gillespie, etc.), it simulate the transformation of reactants into final products for the distribution analysis
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NetBuilder' is a tool for building, visualizing, and simulating multi-layered biological networks, structured as hierarchical Petri-nets. It has a built-in stochastic simulator, but also provides easy access to other simulation and analysis.
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Cell++
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. -
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Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)
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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.
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A platform for the integration of deterministic and stochastic models, for the simulation of the integrated models and for interactive exploration of the model behaviour.
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DNA, Amino Acid And RNA Tests: free software for probabilistic measurement and annotation of biological sequences, using phylogenetic Markov chains and stochastic grammars.
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