• 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...
  • Facile

  • Referenced in 1 article [sw28767]
  • Facile: a command-line network compiler for systems biology. Background: A goal of systems ... biology is the quantitative modelling of biochemical networks. Yet for many biochemical systems, parameter values ... mass action to automatically compile a biochemical network (written as, for example ... analysis of the dynamics of a biochemical network. By acting at the command-line...
  • ANDy

  • Referenced in 2 articles [sw16548]
  • application to toxicity analysis. ANDy , Activity Networks with Delays, is a discrete time framework aimed ... activators, inhibitors or products of biochemical network operation. Activities may have given duration ... represent an object (e.g., an agent, a biochemical species or a family of thereof) with...
  • GRASPER

  • Referenced in 2 articles [sw11757]
  • problem in the context of biochemical networks showing promising results, when compared to an existing...
  • JSBML

  • Referenced in 2 articles [sw13871]
  • storage and exchange of biochemical network models, and is supported by more than 180 software...
  • BioPath

  • Referenced in 4 articles [sw07462]
  • BioPath Biochemical processes in organisms are considered as very large networks consisting of reactants, products ... known Boehringer poster and the Biochemical Pathways atlas. These networks are very complex and grow...
  • 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...
  • LBS

  • Referenced in 15 articles [sw12372]
  • Biochemical Systems (CBS) which affords modular descriptions of metabolic, signalling and regulatory networks in terms...
  • 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 ... investigation of perturbation sites in the biochemical network based on metabolomics data. COVAIN was primarily...
  • CANA

  • Referenced in 2 articles [sw25679]
  • quantifying control and canalization in Boolean Networks. Logical models offer a simple but powerful means ... understand the complex dynamics of biochemical regulation, without the need to estimate kinetic parameters. However ... work we demonstrated that automata network models of biochemical regulation are highly canalizing, whereby many ... criticality of Boolean network dynamics, especially those used to model biochemical regulation (Gates and Rocha...
  • SBtab

  • Referenced in 1 article [sw36554]
  • types can be used to define biochemical network models and the biochemical constants therein...
  • 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...
  • Möbius

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

  • Referenced in 10 articles [sw17247]
  • knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several...
  • scala-smfsb

  • Referenced in 1 article [sw27070]
  • Scala library for stochastic kinetic modelling, biochemical network simulation, and parameter inference, associated with...
  • JigCell

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

  • Referenced in 3 articles [sw16937]
  • iPath: interactive exploration of biochemical pathways and networks. iPath is an open-access online tool...
  • FluxSimulator

  • Referenced in 3 articles [sw25987]
  • Simulate Isotopomer Distributions in Metabolic Networks. The representation of biochemical knowledge in terms of fluxes...
  • Cellerator

  • Referenced in 8 articles [sw09926]
  • extending a computer algebra system to include biochemical arrows for signal transduction simulations. Summary: Cellerator ... networks (STN) with a compact, optionally palette-driven, arrow-based notation to represent biochemical reactions...