• CERENA

  • Referenced in 14 articles [sw19501]
  • simulation and analysis of chemical reaction networks using approximations of the Chemical Master Equation solution ... methods for the analysis of stochastic biochemical reaction networks, focusing on mesoscopic and macroscopic descriptions...
  • SABRE

  • Referenced in 7 articles [sw12884]
  • SABRE: A tool for stochastic analysis of biochemical reaction networks. The importance of stochasticity within ... SABRE, a tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization ... transient solutions of biochemical reaction networks. Biochemical reactions networks represent biological systems studied ... time Markov chains. Besides operating in a stochastic mode, SABRE may also perform a deterministic...
  • COPASI

  • Referenced in 69 articles [sw12253]
  • application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand ... their behavior using ODEs or Gillespie’s stochastic simulation algorithm; arbitrary discrete events...
  • sbioPN

  • Referenced in 5 articles [sw11725]
  • sbioPN: Simulation of deterministic and stochastic spatial biochemical reaction networks using Petri Nets. sbioPN ... simulation of deterministic and stochastic systems of biochemical reaction networks with spatial effects. Models ... Kutta Dormand Prince 45 explicit algorithm. For stochastic solutions, sbioPN offers two variants of Gillespie...
  • smfsb

  • Referenced in 6 articles [sw12260]
  • modelling and simulation of stochastic kinetic biochemical network models. It contains the code and data ... with the second edition of the book Stochastic Modelling for Systems Biology, published by Chapman...
  • HRSSA

  • Referenced in 6 articles [sw18041]
  • HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks. This paper introduces HRSSA ... efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built...
  • sbtoolbox

  • Referenced in 18 articles [sw07391]
  • differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large ... methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis...
  • SPSens

  • Referenced in 1 article [sw24920]
  • software package for stochastic parameter sensitivity analysis of biochemical reaction networks. SPSens is a software ... efficient computation of stochastic parameter sensitivities of biochemical reaction networks. Parameter sensitivity analysis ... many other purposes. However its application to stochastic models has been limited when Monte Carlo ... easily performed on stochastic models of biochemical reaction networks. SPSens implements the algorithms...
  • StochSS

  • Referenced in 6 articles [sw24921]
  • Stochastic Simulation Service. StochSS is an integrated development environment (IDE) for simulation of biochemical networks ... your models from ODE, to well-mixed stochastic, to spatial stochastic. Supports parameter estimation...
  • scala-smfsb

  • Referenced in 1 article [sw27070]
  • scala-smfsb; Scala library for stochastic kinetic modelling, biochemical network simulation, and parameter inference, associated...
  • libSRES

  • Referenced in 2 articles [sw12828]
  • stochastic ranking evolution strategy for parameter estimation. Summary: Estimation of kinetic parameters in a biochemical ... pathway or network represents a common problem in systems studies of biological processes. We have ... biochemical pathways. This library implements a (μ, λ)-ES evolutionary optimization algorithm that uses stochastic...
  • MomentClosure.jl

  • Referenced in 1 article [sw41451]
  • virtually any chemical reaction network or system of stochastic differential equations (SDEs), implementing a wide ... moment closure approximations commonly used in stochastic biochemical kinetics [1]. MomentClosure is (attempted ... omentClosure can be immediately applied to reaction network models defined using Catalyst and SDE systems...
  • HSimulator

  • Referenced in 2 articles [sw22841]
  • biochemical reaction networks. HSimulator is a multithread simulator for mass-action biochemical reaction systems placed ... widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly ... available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA). HRSSA, the fastest hybrid ... simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator...
  • LNA++

  • Referenced in 1 article [sw27627]
  • statistical moments of stochastic chemical reaction networks, a commonly used modeling paradigm describing the probability ... distribution of systems of biochemical species in the intracellular environment. Unlike exact formulations...
  • iNA

  • Referenced in 4 articles [sw17973]
  • which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen ... algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based ... outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with ... stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with...
  • ML-Rules

  • Referenced in 1 article [sw20796]
  • rule-based modeling formalism to model biochemical reaction networks. This repository contains the current version ... Various simulators are available to execute models stochastically (using the SSA or tailored simulators), deterministically...
  • ConvAn

  • Referenced in 2 articles [sw28065]
  • biochemical networks. Dynamic models of biochemical networks usually are described as a system of nonlinear ... most of numerical optimization methods have stochastic properties and the convergence of the objective function...
  • COVAIN

  • Referenced in 1 article [sw10556]
  • univariate and multivariate statistics, network topology and biochemical pathway mapping analysis is in all cases ... Granger time-series analysis, pathway mapping, correlation network topology analysis and visualization, and finally saving ... assumptions of stochastic fluctuations in the metabolic network as described by us recently. By integrating ... systematic investigation of perturbation sites in the biochemical network based on metabolomics data. COVAIN...
  • SeQuaiA

  • Referenced in 0 articles [sw37054]
  • reaction networks (CRNs) play a fundamental role in analysis and design of biochemical systems. They ... induce continuous-time stochastic systems, whose analysis is a computationally intensive task. We present...
  • Coq

  • Referenced in 1880 articles [sw00161]
  • Coq is a formal proof management system. It...