• Bio-PEPA

  • Referenced in 103 articles [sw01361]
  • modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined...
  • COPASI

  • Referenced in 66 articles [sw12253]
  • COPASI: biochemical network simulator. COPASI is a software application for simulation and analysis of biochemical...
  • Celldesigner

  • Referenced in 21 articles [sw09942]
  • diagram editor for gene-regulatory and biochemical networks. CellDesigner is a structured diagram editor ... drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with ... standard for representing models of biochemical and gene-regulatory networks. Networks are able to link...
  • MetaCyc

  • Referenced in 28 articles [sw08243]
  • supporting metabolic engineering, helping to compare biochemical networks, and serving as an encyclopedia of metabolism...
  • COBRA Toolbox

  • Referenced in 13 articles [sw32083]
  • quantitative prediction of cellular and multicellular biochemical networks with constraint-based modelling. It implements ... metabolic phenotypes using genome-scale biochemical networks...
  • Metatool

  • Referenced in 23 articles [sw13278]
  • approaches to calculating elementary modes in biochemical reaction networks have been developed. As a consequence...
  • 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 ... computing transient solutions of biochemical reaction networks. Biochemical reactions networks represent biological systems studied...
  • 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...
  • 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...
  • smfsb

  • Referenced in 6 articles [sw12260]
  • modelling and simulation of stochastic kinetic biochemical network models. It contains the code and data...
  • 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...
  • StochSS

  • Referenced in 5 articles [sw24921]
  • development environment (IDE) for simulation of biochemical networks: Define models in an easy...
  • rBioNet

  • Referenced in 3 articles [sw25730]
  • toolbox extension for reconstructing high-quality biochemical networks. MOTIVATION: Genome-scale metabolic networks are widely ... enabling the construction of publication-level biochemical networks while enforcing necessary quality control measures. rBioNet...
  • Charlie

  • Referenced in 4 articles [sw12881]
  • model validation of natural systems, i.e. biochemical networks, such as metabolic, signal transduction, and gene...
  • DNA

  • Referenced in 7 articles [sw26923]
  • valuable information about the underlying biochemical pathways. Differential network analysis with appropriate connectivity scores...
  • BioMiner

  • Referenced in 3 articles [sw23101]
  • BioMiner - modeling, analyzing, and visualizing biochemical pathways and networks. MOTIVATION: Understanding the biochemistry ... array data grow much faster than biochemical information, it is necessary to infer reactions ... BioMiner--for analyzing and visualizing biochemical pathways and networks. BioMiner is based ... used to model biochemical pathways and networks. As a first application we present PathFinder...
  • ConvAn

  • Referenced in 2 articles [sw28065]
  • convergence analyzing tool for optimization of biochemical networks. Dynamic models of biochemical networks usually...
  • 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...