• smfsb

  • Referenced in 6 articles [sw12260]
  • modelling and simulation of stochastic kinetic biochemical network models. It contains the code and data ... with the second edition of the book Stochastic Modelling for Systems Biology, published by Chapman...
  • BIOCHAM

  • Referenced in 45 articles [sw09927]
  • compatible with SBML); several simulators (boolean, differential, stochastic), a temporal logic based language to formalize ... validate models with respect to such specifications, unique features for developing/correcting/completing/coupling models, including the inference ... kinetic parameters in high dimension from temporal logic constraints. Biocham is a free software protected...
  • Dizzy

  • Referenced in 18 articles [sw35541]
  • solve their models using both ordinary and stochastic differential equation solvers. In addition, Dizzy allows ... models, in order to determine which parameters have the greatest impact on the model kinetics...
  • scala-smfsb

  • Referenced in 1 article [sw27070]
  • scala-smfsb; Scala library for stochastic kinetic modelling, biochemical network simulation, and parameter inference, associated ... with the 3rd edition of the textbook Stochastic Modelling for Systems Biology...
  • StochPy

  • Referenced in 7 articles [sw27252]
  • with stochastic models of gene expression, cell division, and single-molecule enzyme kinetics. StochPy ... been successfully tested against the SBML stochastic test suite, passing all tests. StochPy...
  • Catalyst.jl

  • Referenced in 1 article [sw41453]
  • models, Chemical Langevin SDE models, stochastic chemical kinetics jump process models, and more. Generated models...
  • EIRENE

  • Referenced in 11 articles [sw18048]
  • almost arbitrary complexity. A rather crude model for transport of ionized particles in an externally ... solve more general linear kinetic transport equations, by applying a stochastic rather than a numerical ... particular, options are retained to reduce the model equations to the theoretically important case...
  • SPPARKS

  • Referenced in 8 articles [sw04146]
  • SPPARKS, an acronym for Stochastic Parallel PARticle Kinetic Simulator. SPPARKS is a parallel Monte Carlo ... code for on-lattice and off-lattice models that includes algorithms for kinetic Monte Carlo...
  • STOCKS

  • Referenced in 13 articles [sw10438]
  • Gillespie algorithm. STOCKS, software for the stochastic kinetic simulation of biochemical processes is presented ... application of a simple cell division model. Taking expression of Escherichia coli beta-galactosidase...
  • Cyto-Sim

  • Referenced in 5 articles [sw35368]
  • processes. Results: We present Cyto-Sim, a stochastic simulator of membrane-enclosed hierarchies of biochemical ... inner, outer and integral layer. The underlying model is based on formal language theory ... variable levels of abstraction via arbitrary chemical kinetics which link to ordinary differential equations...
  • SELM

  • Referenced in 3 articles [sw17574]
  • solvent coarse-grained (IS-CG) models by incorporating kinetic contributions from the solvent to facilitate ... methods based on fluctuating hydrodynamics and the stochastic Eulerian Lagrangian method (SELM). SELM couples ... grained microstructure degrees of freedom to continuum stochastic fields to capture both the relaxation ... graphical user interface (GUI) for setting up models and simulations, (iv) standardized XML formats...
  • ML-Rules

  • Referenced in 1 article [sw20796]
  • solutions. Further, ML-Rules supports arbitrary reaction kinetics. ML-Rules is implemented as an external ... Various simulators are available to execute models stochastically (using the SSA or tailored simulators), deterministically...
  • kTAM

  • Referenced in 1 article [sw22257]
  • Patitz (2012) [22]), numerical simulations of the kinetic counterpart have been performed only ... using classical stochastic simulation algorithms frameworks, which are not designed for capturing models with theoretically ... such type of modelling. We show not only how the modelling of kTAM ... explore the advantages of this modelling framework for kinetic simulations of kTAM and the easy...
  • MomentClosure.jl

  • Referenced in 1 article [sw41451]
  • moment closure approximations commonly used in stochastic biochemical kinetics [1]. MomentClosure is (attempted ... immediately applied to reaction network models defined using Catalyst and SDE systems built with ModelingToolkit...
  • SGNS2

  • Referenced in 2 articles [sw34966]
  • Motivation: Cell growth and division affect the kinetics of internal cellular processes and the phenotype ... chemical reaction systems according to the Stochastic Simulation Algorithm with multi-delayed reactions within hierarchical ... basis. We exemplify its use with six models including a stochastic model of the disposal...
  • PLATYPUS

  • Referenced in 1 article [sw26744]
  • three-dimensional classical dynamical reaction model with stochastic breakup is presented, which is a useful ... breakup observables, such as angle, kinetic energy and relative energy distributions...
  • bsmKinetic

  • Referenced in 0 articles [sw22296]
  • stochastic point-transition model. We introduce bsmKinetic, an implementation of the stochastic multichannel point-transition ... approach to simulation of the charge transfer kinetics in molecular systems with reorganization of many...
  • ADmoND

  • Referenced in 1 article [sw31429]
  • treated as a deterministic or a stochastic one. Some system parameters are stored ... choose calculations applicable to nonlinear model of adsorption based on nonlinear Riccati equations or calculations ... linear Lagergren pseudo first order kinetic model. Button Hold Toggle aims for keeping or discarding ... equilibrium coverage and power spectral densities of stochastic variables in the system. Genuinely, the number...
  • ASCOT

  • Referenced in 1 article [sw16815]
  • guiding center solution of the kinetic equation applying stochastic differential equations in the presence ... code, which has made implementation of additional models impractical. Also, a benchmark between the previous...
  • laurenzi

  • Referenced in 1 article [sw26905]
  • this paper, we employ the stochastic approach to chemical kinetics to construct the pause time ... formulate robust estimators of the parameters of models for the force-dependence...