• KEGG

  • Referenced in 275 articles [sw13866]
  • molecular wiring diagrams of interaction, reaction and relation networks (systems information). It also contains disease...
  • FLASH

  • Referenced in 71 articles [sw17500]
  • equations of state and thermonuclear reaction networks. The FLASH code was developed to study...
  • Metatool

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

  • Referenced in 14 articles [sw19501]
  • CERENA (ChEmical REaction Network Analyzer) is a MATLAB-based toolbox for the simulation and analysis ... chemical reaction networks using approximations of the Chemical Master Equation solution statistics. CERENA includes ... analysis of stochastic biochemical reaction networks, focusing on mesoscopic and macroscopic descriptions, namely Reaction Rate...
  • MIN3P

  • Referenced in 13 articles [sw11519]
  • respect to the definition of the reaction network. Advective-diffusive transport in the water phase ... phase are included. Equilibrium reactions considered are aqueous complexation, gas partitioning between phases, oxidation-reduction ... exchange, and surface complexation. The reaction network is designed to handle kinetically controlled intra-aqueous...
  • crntwin

  • Referenced in 17 articles [sw14624]
  • CRNTWin. The chemical reaction network toolbox...
  • CoNtRol

  • Referenced in 11 articles [sw14067]
  • framework for the analysis of chemical reaction networks. Summary: We introduce CoNtRol, a web-based ... framework for analysis of chemical reaction networks (CRNs). It is designed to be both extensible...
  • SABRE

  • Referenced in 7 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...
  • Data2Dynamics

  • Referenced in 12 articles [sw25272]
  • construct dynamical models of biochemical reaction networks for large datasets and complex experimental conditions...
  • Paramotopy

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

  • Referenced in 7 articles [sw06416]
  • explore algebraic methods for bio-chemical reaction networks Given a bio-chemical reaction network...
  • CRNreals

  • Referenced in 5 articles [sw13616]
  • distinguishability and identifiability analysis of biochemical reaction networks. Chemical reaction network theory is widely used ... analyzing complex biochemical systems such as metabolic networks and cell signalling pathways. Being able ... chemically important qualitative dynamical features, chemical reaction networks (CRNs) have attracted significant attention...
  • HRSSA

  • Referenced in 6 articles [sw18041]
  • stochastic simulation for spatially homogeneous biochemical reaction networks. This paper introduces HRSSA (Hybrid Rejection-based ... simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA ... relies on propensity bounds to select next reaction firings and to reduce the average number...
  • MedOlDatschgerl

  • Referenced in 6 articles [sw16744]
  • graph transformation system for automatically generating reaction networks from graph grammar formulations of chemistries ... automatically visualise molecules, reactions, and reaction networks. Examples of how to use the Python interface...
  • sbioPN

  • Referenced in 5 articles [sw11725]
  • deterministic and stochastic spatial biochemical reaction networks using Petri Nets. sbioPN is a package suited ... deterministic and stochastic systems of biochemical reaction networks with spatial effects. Models are defined using ... that is close at how chemical reactions are defined. For deterministic solutions, sbioPN creates...
  • parest_dae

  • Referenced in 7 articles [sw09087]
  • Practiced. Chemical mechanisms for even simple reaction networks involve many highly reactive and short-lived ... QSSA is ubiquitous in modeling enzymatic reactions. In this chapter, we focus attention...
  • Cantera

  • Referenced in 28 articles [sw15111]
  • interfaces between these phases, reaction managers, time-dependent reactor networks, and steady one-dimensional reacting...
  • ERODE

  • Referenced in 6 articles [sw20210]
  • most two, covering elementary chemical reaction networks (CRNs) and continuous time Markov chains (CTMCs...
  • Ernest

  • Referenced in 3 articles [sw13872]
  • Ernest: a toolbox for chemical reaction network theory. Summary: ERNEST Reaction Network Equilibria Study Toolbox ... structure of a chemical reaction network, can exclude the multistationarity of the corresponding reaction system...
  • expa

  • Referenced in 3 articles [sw35555]
  • calculating extreme pathways in biochemical reaction networks. Summary: The set of extreme pathways, a generating ... state flux maps in a biochemical reaction network, can be computed from the stoichiometric matrix ... with a Windows executable and sample network reaction files, are available at http://systemsbiology.ucsd.edu...