
BioPEPA
 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 generegulatory and biochemical networks. CellDesigner is a structured diagram editor ... drawing generegulatory and biochemical networks. Networks are drawn based on the process diagram, with ... standard for representing models of biochemical and generegulatory 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 constraintbased modelling. It implements ... metabolic phenotypes using genomescale 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 highquality biochemical networks. MOTIVATION: Genomescale metabolic networks are widely ... enabling the construction of publicationlevel 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 ... BioMinerfor 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 ... steadystate flux maps in a biochemical reaction network, can be computed from the stoichiometric...