• KEGG

  • Referenced in 260 articles [sw13866]
  • chemical information) that are integrated with the knowledge on molecular wiring diagrams of interaction, reaction ... relation networks (systems information). It also contains disease and drug information (health information) as perturbations...
  • CERENA

  • Referenced in 13 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...
  • crntwin

  • Referenced in 16 articles [sw14624]
  • CRNTWin. The chemical reaction network toolbox...
  • CoNtRol

  • Referenced in 10 articles [sw14067]
  • source framework for the analysis of chemical reaction networks. Summary: We introduce CoNtRol ... based framework for analysis of chemical reaction networks (CRNs). It is designed to be both...
  • PoCaB

  • Referenced in 7 articles [sw06416]
  • explore algebraic methods for bio-chemical reaction networks Given a bio-chemical reaction network ... derived database called PoCaB (Platform of Chemical and Biological data). We also present a visualization...
  • CRNreals

  • Referenced in 3 articles [sw13616]
  • distinguishability and identifiability analysis of biochemical reaction networks. Chemical reaction network theory is widely used ... chemically important qualitative dynamical features, chemical reaction networks (CRNs) have attracted significant attention...
  • ERODE

  • Referenced in 5 articles [sw20210]
  • degree at most two, covering elementary chemical reaction networks (CRNs) and continuous time Markov chains...
  • CRNSimulator

  • Referenced in 3 articles [sw33636]
  • Mathematica package for working with networks of coupled chemical reactions. It forms ... foundation for syntactic manipulation of chemical reaction networks as Mathematica expressions. It allows mixing ... simulate experiments in which a sequence of chemical additions is performed. It is particularly well ... engineered chemical systems, in which chemical reaction networks can be used as a kind...
  • Ernest

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

  • Referenced in 4 articles [sw29331]
  • differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup...
  • SeQuaiA

  • Referenced in 1 article [sw37054]
  • tool for semi-quantitative analysis of chemical reaction networks. Chemical reaction networks (CRNs) play...
  • crnpy

  • Referenced in 2 articles [sw23179]
  • manipulation and analysis of chemical reaction networks...
  • parest_dae

  • Referenced in 7 articles [sw09087]
  • Taught and as Practiced. Chemical mechanisms for even simple reaction networks involve many highly reactive ... products, present in larger concentrations. The chemical mechanism also often contains many rate constants whose ... QSSA is ubiquitous in modeling enzymatic reactions. In this chapter, we focus attention...
  • KINSOLVER

  • Referenced in 1 article [sw00488]
  • living system is as a chemical reaction network, and new genomics technologies like ... ways to measure the state of these networks. The goal here is being able ... ensemble of hypothesized biochemical and genetic regulatory networks to predict what a cell is doing ... system.\parThe simulator KINSOLVER solves chemical reaction networks, satisfying standard multiplicative mass-action kinetics...
  • Cantera

  • Referenced in 22 articles [sw15111]
  • object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. Cantera provides ... interfaces between these phases, reaction managers, time-dependent reactor networks, and steady one-dimensional reacting...
  • nuskell

  • Referenced in 1 article [sw22846]
  • translation wrapper function. A formal chemical reaction network (CRN) is translated into a domain-level...
  • LNA++

  • Referenced in 1 article [sw27627]
  • statistical moments of stochastic chemical reaction networks, a commonly used modeling paradigm describing the probability ... computationally feasible even for CRNs with many reaction events. The tractability ... common choice for inference of unknown chemical reaction parameters. However, this task is impeded...
  • Chempl

  • Referenced in 1 article [sw34077]
  • modeling usually involves handling of a chemical reaction network and solution...
  • Z34Bio

  • Referenced in 1 article [sw25444]
  • illustrate through the treatment of chemical reaction networks and Boolean networks. We present case-studies...