• COPASI

  • Referenced in 53 articles [sw12253]
  • behavior using ODEs or Gillespie’s stochastic simulation algorithm; arbitrary discrete events can be included...
  • XPPAUT

  • Referenced in 353 articles [sw05543]
  • XPPAUT is software for the analysis and simulation of dynamic systems. It includes AUTO ... other useful routines. Differential equations, maps, stochastic systems, delay equations, integral equations, and other systems...
  • sde

  • Referenced in 42 articles [sw23230]
  • package sde: Simulation and Inference for Stochastic Differential Equations. Companion package to the book Simulation...
  • MesoRD

  • Referenced in 27 articles [sw18202]
  • Stochastic reaction-diffusion simulation with MesoRD ... Summary: MesoRD is a tool for stochastic simulation of chemical reactions and diffusion. In particular...
  • URDME

  • Referenced in 24 articles [sw10400]
  • Urdme: a modular framework for stochastic simulation of reaction-transport processes in complex geometries ... software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular...
  • ASA

  • Referenced in 73 articles [sw04736]
  • Adaptive Simulated Annealing (ASA) is a C-language code developed to statistically find the best ... robust tuning over many classes of nonlinear stochastic systems...
  • STEPS

  • Referenced in 18 articles [sw17866]
  • simulation platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex...
  • gss

  • Referenced in 240 articles [sw06099]
  • spline ANOVA models Nonparametric function estimation with stochastic data, otherwise known as smoothing, has been ... facilities is illustrated in the book through simulated and real data examples...
  • BIOCHAM

  • Referenced in 40 articles [sw09927]
  • systems (compatible with SBML); several simulators (boolean, differential, stochastic), a temporal logic based language...
  • sbtoolbox

  • Referenced in 16 articles [sw07391]
  • build applications for the analysis and simulation of biological and biochemical systems. Additionally ... analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis...
  • SSJ

  • Referenced in 11 articles [sw08862]
  • framework for stochastic simulation in Java. We introduce SSJ, an organized set of software tools ... offering general-purpose facilities for stochastic simulation programming. It supports the event view, process view...
  • GillespieSSA

  • Referenced in 9 articles [sw21016]
  • package GillespieSSA: Gillespie’s Stochastic Simulation Algorithm (SSA). GillespieSSA provides a simple to use, intuitive ... extensible interface to several stochastic simulation algorithms for generating simulated trajectories of finite population continuous ... Currently it implements Gillespie’s exact stochastic simulation algorithm (Direct method) and several approximate methods...
  • StochKit

  • Referenced in 10 articles [sw06978]
  • StochKit is an extensible stochastic simulation framework developed in C++ that aims to make stochastic ... simulation accessible to practicing biologists and chemists, while remaining open to extension via new stochastic...
  • COMPASS

  • Referenced in 33 articles [sw03040]
  • measure is estimated via a stochastic, discrete-event simulation, and the decision variables are integer...
  • STOCKS

  • Referenced in 13 articles [sw10438]
  • STOCKS: STOChastic kinetic simulations of biochemical systems with Gillespie algorithm. STOCKS, software for the stochastic...
  • StochKit2

  • Referenced in 8 articles [sw14081]
  • StochKit2: software for discrete stochastic simulation of biochemical systems with events. Summary: StochKit2 ... major upgrade of the popular StochKit stochastic simulation software package. StochKit2 provides highly efficient implementations ... several variants of Gillespie’s stochastic simulation algorithm (SSA), and tau-leaping with automatic step...
  • SGN Sim

  • Referenced in 8 articles [sw29325]
  • stochastic genetic networks simulator. We present SGNSim, ’Stochastic Gene Networks Simulator’, a tool to model ... dynamics is driven by a stochastic simulation algorithm (SSA) able to deal with multiple time...
  • HRSSA

  • Referenced in 6 articles [sw18041]
  • HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks. This paper introduces HRSSA ... Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially ... RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction...
  • STOCHSIMGPU

  • Referenced in 6 articles [sw10711]
  • STOCHSIMGPU: parallel stochastic simulation for the systems biology toolbox 2 for Matlab. STOCHSIMGPU ... many realisations, so called ensemble, of stochastic simulations of chemical reaction systems in parallel ... MATLAB and replaces its stochastic simulation code seamlessly. This means, you can benefit from using ... STOCHSIMGPU which exploits GPUs for parallel stochastic simulations of biological/chemical reaction systems and show that...
  • NMOF

  • Referenced in 10 articles [sw11303]
  • options, and functions that help with stochastic simulations...