• COPASI

  • Referenced in 69 articles [sw12253]
  • their behavior using ODEs or Gillespie’s stochastic simulation algorithm; arbitrary discrete events...
  • STOCKS

  • Referenced in 13 articles [sw10438]
  • kinetic simulations of biochemical systems with Gillespie algorithm. STOCKS, software for the stochastic kinetic simulation ... program uses a rigorously derived Gillespie algorithm that has been shown to be applicable...
  • GillespieSSA

  • Referenced in 10 articles [sw21016]
  • package GillespieSSA: Gillespie’s Stochastic Simulation Algorithm (SSA). GillespieSSA provides a simple to use, intuitive ... model. Currently it implements Gillespie’s exact stochastic simulation algorithm (Direct method) and several approximate...
  • EoN

  • Referenced in 6 articles [sw31396]
  • weighted graphs; allows non-Markovian dynamics; Gillespie algorithms for Markovian dynamics; Through some careful optimization...
  • sbioPN

  • Referenced in 5 articles [sw11725]
  • solutions, sbioPN offers two variants of Gillespie algorithm, or SSA. For hybrid deterministic/stochastic, it employs...
  • MaBoSS

  • Referenced in 4 articles [sw34208]
  • applies Monte-Carlo kinetic algorithm (or Gillespie algorithm) to the network to produce time trajectories...
  • StochKit2

  • Referenced in 11 articles [sw14081]
  • implementations of several variants of Gillespie’s stochastic simulation algorithm (SSA), and tau-leaping with...
  • RNAexpNumNbors

  • Referenced in 1 article [sw23799]
  • folding kinetics using Monte Carlo and Gillespie algorithms. RNA secondary structure folding kinetics is known ... Monte Carlo algorithm or the Gillespie algorithm. Here we investigate the relation between the Monte ... Carlo algorithm and the Gillespie algorithm. We prove that asymptotically, the expected time ... times that of the Gillespie algorithm, where 〈N〉 denotes the Boltzmann expected network degree...
  • Gillespie.jl

  • Referenced in 2 articles [sw28297]
  • direct method (sometimes called the Doob-Gillespie algorithm) (Doob 1945; Gillespie 1977), an approach widely...
  • BioSimulator.jl

  • Referenced in 2 articles [sw28296]
  • extinction, complicate system dynamics. Stochastic simulation algorithms are useful in generating time-evolution trajectories ... flexible package, BioSimulator.jl, for implementing the Gillespie algorithm, τ-leaping, and related stochastic simulation algorithms...
  • KFOLD

  • Referenced in 1 article [sw23800]
  • implementation of the Gillespie algorithm for RNA kinetics with logarithmic time update. In this paper ... KINFOLD algorithm, which also uses the Gillespie algorithm to predict folding kinetics, KFOLD stochastically chooses ... addition/deletion following the Gillespie procedure. However, unlike KINFOLD, the KFOLD algorithm utilizes the fact that...
  • KaSim

  • Referenced in 2 articles [sw29287]
  • state simulation algorithm [10] which adapts Gillespie’s algorithm [21, 22] to rule-based models...
  • ppsim

  • Referenced in 1 article [sw38637]
  • exact* stochastic dynamics. ppsim implements this algorithm, with a tightly optimized Cython implementation that ... dynamically switches to the CRN Gillespie algorithm for efficiency gains when the number of applicable...
  • OpenEPSim

  • Referenced in 1 article [sw33217]
  • system is then simulated using the Gillespie algorithm, and time-averaged statistics collected...
  • Tyche

  • Referenced in 1 article [sw23577]
  • Method (based in turn on the Gillespie algorithm). This models stochastic diffusion, and reactions...
  • scModels

  • Referenced in 1 article [sw41031]
  • kind). Three different implementations of the Gillespie algorithm allow data simulation based on the basic...
  • PALOMA

  • Referenced in 2 articles [sw20657]
  • model which including stochastic simulation using Gillespie’s algorithm and moment-closure approximation by exporting...
  • GillesPy

  • Referenced in 1 article [sw42018]
  • construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model ... simulation algorithms based on the Gillespie stochastic simulation algorithms. To enable intuitive model construction...
  • Mathematica

  • Referenced in 6343 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 13488 articles [sw00558]
  • MATLAB® is a high-level language and interactive...