• Metatool

  • Referenced in 23 articles [sw13278]
  • approaches to calculating elementary modes in biochemical reaction networks have been developed. As a consequence...
  • CERENA

  • Referenced in 13 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 6 articles [sw12884]
  • tool for stochastic analysis of biochemical reaction networks. The importance of stochasticity within biological systems ... tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization ... algorithm for computing transient solutions of biochemical reaction networks. Biochemical reactions networks represent biological systems...
  • Paramotopy

  • Referenced in 12 articles [sw08781]
  • number of equilibria of a biochemical reaction network depends on the choice of a number...
  • Data2Dynamics

  • Referenced in 11 articles [sw25272]
  • construct dynamical models of biochemical reaction networks for large datasets and complex experimental conditions...
  • HRSSA

  • Referenced in 6 articles [sw18041]
  • hybrid stochastic simulation for spatially homogeneous biochemical reaction networks. This paper introduces HRSSA (Hybrid Rejection ... stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built...
  • sbioPN

  • Referenced in 5 articles [sw11725]
  • Simulation of deterministic and stochastic spatial biochemical reaction networks using Petri Nets. sbioPN ... deterministic and stochastic systems of biochemical reaction networks with spatial effects. Models are defined using...
  • expa

  • Referenced in 3 articles [sw35555]
  • program for calculating extreme pathways in biochemical reaction networks. Summary: The set of extreme pathways ... steady-state flux maps in a biochemical reaction network, can be computed from the stoichiometric...
  • CRNreals

  • Referenced in 3 articles [sw13616]
  • distinguishability and identifiability analysis of biochemical reaction networks. Chemical reaction network theory is widely used ... modeling and analyzing complex biochemical systems such as metabolic networks and cell signalling pathways. Being ... chemically important qualitative dynamical features, chemical reaction networks (CRNs) have attracted significant attention...
  • HSimulator

  • Referenced in 2 articles [sw22841]
  • HSimulator: hybrid stochastic/deterministic simulation of biochemical reaction networks. HSimulator is a multithread simulator for mass ... action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation ... simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator...
  • IBRENA

  • Referenced in 1 article [sw30481]
  • silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks ... present In silico Biochemical Reaction Network Analysis (IBRENA), a software package which facilitates multiple functions ... including cellular reaction network simulation and sensitivity analysis (both forward and adjoint methods), coupled with ... formulation, testing and reduction of theoretical biochemical reaction networks, the program can also be used...
  • SPSens

  • Referenced in 1 article [sw24920]
  • stochastic parameter sensitivity analysis of biochemical reaction networks. SPSens is a software package ... computation of stochastic parameter sensitivities of biochemical reaction networks. Parameter sensitivity analysis is a valuable ... easily performed on stochastic models of biochemical reaction networks. SPSens implements the algorithms...
  • JigCell

  • Referenced in 2 articles [sw35661]
  • Builder (JCMB), a tool for creating biochemical reaction network models. JCMB is designed for ease...
  • Möbius

  • Referenced in 23 articles [sw04098]
  • reliability, availability, and performance of computer and network systems, its use has expanded rapidly ... range of discrete-event systems, from biochemical reactions within genes to the effects of malicious...
  • LBS

  • Referenced in 15 articles [sw12372]
  • Biochemical Systems (CBS) which affords modular descriptions of metabolic, signalling and regulatory networks in terms ... reactions between modified complexes, occurring concurrently inside a hierarchy of compartments and with possible cross...
  • ML-Rules

  • Referenced in 1 article [sw20796]
  • rule-based modeling formalism to model biochemical reaction networks. This repository contains the current version...
  • sbtoolbox

  • Referenced in 17 articles [sw07391]
  • equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large number ... deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis...
  • BioPath

  • Referenced in 4 articles [sw07462]
  • BioPath Biochemical processes in organisms are considered as very large networks consisting of reactants, products ... reactions and regulation. Examples are given by the well-known Boehringer poster and the Biochemical ... Pathways atlas. These networks are very complex and grow fast by the steady progress...
  • Cellerator

  • Referenced in 8 articles [sw09926]
  • networks (STN) with a compact, optionally palette-driven, arrow-based notation to represent biochemical reactions...
  • DistributedFBA

  • Referenced in 0 articles [sw17709]
  • predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks...