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gillespie-algorithm
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Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
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Mar 29, 2020 - AMPL
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
systems-biology
moments
chemical-reaction-networks
stochastic-processes
gene-network
gillespie-algorithm
moment-equations
moment-closure
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Sep 1, 2021 - Julia
Finite State Projection algorithms for chemical reaction networks
systems-biology
julia-package
chemical-reaction-networks
gene-network
gillespie-algorithm
stochastic-simulations
biological-modeling
finite-state-projection
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Aug 23, 2021 - Julia
Catalyst.jl importers for various reaction network file formats.
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Aug 31, 2021 - Julia
Networkx implementation of the SIS epidemic model for large and heterogeneous networks
networkx
computational-physics
complex-networks
epidemics
stochastic-processes
stochastic-simulation-algorithm
markovian-epidemic-processes
gillespie-algorithm
markovian-processes
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Jul 26, 2017 - Python
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
systems-biology
ode
differential-equations
chemical-reaction-networks
sbml
gillespie-algorithm
quantitative-systems-pharmacology
sciml
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Updated
Sep 1, 2021 - Julia
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Nov 25, 2020 - C++
viterbi-algorithm
computational-biology
gene-expression
smith-waterman
alternative-splicing
gradient-descent
differential-expression
gillespie
genome-analysis
gradient-descent-algorithm
bowtie2
differential-analysis
single-cell-genomics
gillespie-algorithm
single-cell-analysis
gradient-descent-implementation
genome-alignment
viterbi-decoder
smith-waterman-alignment
differential-expression-analysis
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Dec 21, 2019 - Jupyter Notebook
A free, open-source tool for modeling chemical reaction networks in Python
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Jan 24, 2020 - Python
Stochastic implementation of a Lotka-Volterra competition model extended to multidimensional niche spaces (published in 10.1103/PhysRevE.91.052107)
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Apr 13, 2018 - C
Implementation of SIS epidemic model for large and heterogeneous networks.
networkx
computational-physics
complex-networks
epidemics
stochastic-processes
stochastic-simulation-algorithm
markovian-epidemic-processes
gillespie-algorithm
markovian-processes
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Nov 30, 2017 - Fortran
Gillespie algorithm implementing the ARN-Protein model for multiple cells.
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Jun 10, 2020 - C++
Numba accelerated implementation of Gillespie's algorithm for simulating stochastic processes
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Apr 28, 2021 - Python
Working with Gillespie algorithm in order to exam Double step gene expression model.
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Apr 1, 2021 - Python
A Matlab library of numerical methods for solving differential equations stochastically and continuously .
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Nov 12, 2017 - MATLAB
automatized generation of optimized Gillespie algorithm
dependency-graph
data-structures
binary-search-tree
nonlinear-dynamics
temporal-data
kinetic-modeling
reduction-strategies
gillespie-algorithm
pathway-models
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Aug 18, 2018 - Fortran
Shiny app simulating stochastic epidemics with Gillespie's direct method.
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Jul 30, 2019 - R
A simulation of the propagation of a virus using the Gillespie algorithm
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Jun 11, 2020 - C++
Final Project for a Mathematical Biology course
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Aug 4, 2017 - TeX
Fortran implementation of the Krylov-FSP-SSA algorithm for solving the Chemical Master Equation.
numerical-methods
stochastic-simulation-algorithm
gillespie-algorithm
krylov-subspace-approximation
chemical-master-equation
stochastic-reaction-networks
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Jul 29, 2021 - Fortran
Efficient discrete random distribution for C++. The implementation uses array-based sum tree to allow fast sampling and updates of weighted events.
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Dec 28, 2020 - C++
Delay Gillespie Degrade and Fire with variable delay
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Feb 11, 2021 - Python
Gillespie simulations of advantageous drivers & deleterious passengers in cancer
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Feb 4, 2019 - C
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Apr 18, 2019 - Python
Models for Biochemical and Biophysical Research Communications manuscript
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Aug 21, 2018
Implementation of SIS epidemic model for large and heterogeneous networks
networkx
computational-physics
complex-networks
epidemics
stochastic-processes
stochastic-simulation-algorithm
markovian-epidemic-processes
gillespie-algorithm
markovian-processes
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Jul 26, 2017 - Python
Scalable stochastic simulation of chemical networks
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Jun 4, 2020 - Jupyter Notebook
Bayesian inference of stochastic cellular processes with and without memory in Python.
python
markov-model
statistical-inference
model-selection
biological-data-analysis
dynamical-systems
parameter-estimation
bayesian-inference
nested-sampling
stochastic-processes
probabilistic-models
gillespie-algorithm
stochastic-models
master-equation
biological-modeling
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May 25, 2021 - Python
Gillespie Codes on Lattices in C++
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Jul 6, 2021 - Mathematica
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The package currently exports these function names:
mm,mmr,hill,hillr,hillar.To avoid these potentially overwriting other stuff people have decalred, they could be moved to some other sub package. They would then be imported using e.g.