GitHub topics: stochastic-simulation-algorithm

Repositories

biocircuits/bioscrape

BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation)

Language: Jupyter Notebook - Size: 180 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 29 - Forks: 19

SystemsBioinformatics/stochpy

StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

Language: Python - Size: 395 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 42 - Forks: 11

VishvasRanjan/Learning-Chemical-Reaction-Networks-CRNs

This repository contains the work that was conducted under the joint supervision of Dr. Behera and Prof. Sbalzarini at the Sbalzarini Lab, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) and the Center for Systems Biology Dresden (CSBD).

Language: Jupyter Notebook - Size: 10.2 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0

crflynn/stochastic

Generate realizations of stochastic processes in python.

Language: Python - Size: 3.73 MB - Last synced at: 21 days ago - Pushed at: over 2 years ago - Stars: 478 - Forks: 88

alexplaka/AbStochKin

Agent-based Stochastic Kinetics

Language: Python - Size: 20.6 MB - Last synced at: 9 days ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

xiaomingfu2013/DelaySSAToolkit.jl

DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays

Language: Julia - Size: 9.41 MB - Last synced at: 7 days ago - Pushed at: 2 months ago - Stars: 16 - Forks: 5

DiODeProject/MuMoT

Multiscale Modelling Tool - mathematical modelling without the maths

Language: Python - Size: 31.6 MB - Last synced at: 2 days ago - Pushed at: over 3 years ago - Stars: 22 - Forks: 6

rte-antares-rpackage/antaresViz

ANTARES Visualizations

Language: R - Size: 5.65 MB - Last synced at: 5 days ago - Pushed at: 6 months ago - Stars: 21 - Forks: 11

Jamesflynn1/pyRBM

A Python framework to build and simulate stochastic rules-based models.

Language: Jupyter Notebook - Size: 1.15 MB - Last synced at: 2 days ago - Pushed at: 8 months ago - Stars: 3 - Forks: 0

fvalle1/nsbm

nSBM: multi branch topic modeling

Language: Jupyter Notebook - Size: 16.5 MB - Last synced at: 3 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 2

danieljsharpe/DISCOTRESS_tutorials

Learn to get started using DISCOTRESS with these tutorials! Then apply to your own Markov chains in ecology 🦜🌴 economics 💸📈 biophysics 🧬🦠 and more!

Language: Brainfuck - Size: 5.43 MB - Last synced at: 3 months ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 2

danieljsharpe/DISCOTRESS

🦜 DISCOTRESS 🦜 is a software package to simulate and analyse the dynamics on arbitrary Markov chains

Language: C++ - Size: 4.35 MB - Last synced at: 3 months ago - Pushed at: almost 4 years ago - Stars: 25 - Forks: 5

wcota/dynSIS

Implementation of SIS epidemic model for large and heterogeneous networks using Fortran.

Language: Fortran - Size: 1.51 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 9 - Forks: 2

rafaelstjf/STOCBIONET

STOCBIONET is a software for stochastic simulation of biochemical networks

Language: C++ - Size: 2.71 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1

ctogle/mini_gillespiem

Scalable stochastic simulation of chemical networks

Language: Jupyter Notebook - Size: 2.66 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

EDS-Bioinformatics-Laboratory/GillespieExamples

Antoine van Kampen: Examples of the Gillespie algorithm

Size: 19.5 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

HadrienNU/LangevinIntegrators.jl

A set of integrators for the Langevin equation.

Language: Julia - Size: 725 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

wcota/dynSIS-networkx

Networkx implementation of the SIS epidemic model for large and heterogeneous networks

Language: Python - Size: 28.3 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 14 - Forks: 4

locuoco/stochastic-chemical-kinetics

Stochastic chemical kinetics using Gillespie algorithm and chemical master equation, application to enzyme kinetics

Language: C++ - Size: 4.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

wcota/dynSIS-py

Implementation of SIS epidemic model for large and heterogeneous networks

Language: Python - Size: 32.2 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 4

wcota/dynSIS-GA

Implementation of SIS epidemic model with a Gillespie Algorithm - NOT optimized

Language: Fortran - Size: 28.3 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1

voduchuy/KrylovFspSsa

Fortran implementation of the Krylov-FSP-SSA algorithm for solving the Chemical Master Equation.

Language: Fortran - Size: 71.3 KB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

sschoeller/R-chemical-kinetics

Stochastic Simulation of Chemical Kinetics

Language: R - Size: 4.88 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

ManuelaCarriero/PyExTra

Implementation of algorithms for simulating gene expression and translation in order to investigate about NF-kB model in colon cancer cells.

Language: TeX - Size: 19.7 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

lepton01/stochastic

Repository for stochastic methods scripts and functions.

Language: Julia - Size: 44.9 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

lillux/gillespie_ssa

Implementation of Gillespie Stochastic Simulation Algorithm

Language: Jupyter Notebook - Size: 495 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

Gapouliasis/Stochastic-Models

Usefull models simulating stochastic processes in different times scales with or without reproduction of long-term percistence (Hurst-Kolmogorov behaviour). Also a simple tool for determening the Hurst coefficient is provided. All code is in the form of Matlab functions.

Language: Matlab - Size: 11.7 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 1