• COPASI

  • Referenced in 71 articles [sw12253]
  • simulator. COPASI is a software application for simulation and analysis of biochemical networks and their ... that supports models in the SBML standard and can simulate their behavior using ODEs...
  • BIOCHAM

  • Referenced in 45 articles [sw09927]
  • modeling biochemical systems (compatible with SBML); several simulators (boolean, differential, stochastic), a temporal logic based...
  • Celldesigner

  • Referenced in 22 articles [sw09942]
  • stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical ... networks. Networks are able to link with simulation and other analysis packages through Systems Biology ... integration with SBML ODE Solver, SBML Simulation Core and Copasi. By using CellDesigner ... modify existing SBML models with references to existing databases, simulate and view the dynamics through...
  • StochPy

  • Referenced in 7 articles [sw27252]
  • cell biology. It provides various stochastic simulation algorithms, SBML support, analyses of the probability distributions ... statistical functions and plotting facilities for stochastic simulations. We illustrate the functionality of StochPy with ... StochPy has been successfully tested against the SBML stochastic test suite, passing all tests. StochPy ... comprehensive software package for stochastic simulation of the molecular control networks of living cells...
  • libRoadRunner

  • Referenced in 4 articles [sw34670]
  • LibRoadRunner: A high performance SBML simulation and analysis library...
  • SBML-SAT

  • Referenced in 7 articles [sw21897]
  • freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady state analysis, robustness...
  • LibSBMLSim

  • Referenced in 1 article [sw41444]
  • reference implementation of fully functional SBML simulator. Motivation: The Systems Biology Markup Language (SBML ... library that supports all features of SBML for simulating ODE models. Therefore, a demand exists ... implementation of a numerical integrator that supports SBML to enhance the development of a computational...
  • SBMLSim

  • Referenced in 1 article [sw41896]
  • sbmlsim: SBML simulation made easy. The idea of sbmlsim is to provide a simple abstraction ... layer for running simulations with SBML models in python and simplify common tasks occuring...
  • sbtoolbox

  • Referenced in 18 articles [sw07391]
  • build applications for the analysis and simulation of biological and biochemical systems. Additionally ... toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import ... toolbox connects nicely to other SBML-enabled modelling packages. Models are represented in an internal ... analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis...
  • MASSpy

  • Referenced in 1 article [sw41441]
  • libRoadRunner: the Systems Biology Markup Language (SBML) simulation engine. Three examples are provided to demonstrate...
  • SBML-PET

  • Referenced in 2 articles [sw12829]
  • model. SBML models can also be simulated in SBML-PET. Stochastic Ranking Evolution Strategy (SRES...
  • SBMLsimulator

  • Referenced in 1 article [sw13435]
  • SBML. SBMLsimulator is a fast, accurate, and easily usable program for dynamic model simulation ... Systems Biology Markup Language (SBML). For simulation it contains the Systems Biology Simulation Core Library ... which has been benchmarked against the entire SBML Test Suite and all models from ... source library JSBML. The integrated Systems Biology Simulation Core Library can be obtained...
  • CaliBayes

  • Referenced in 1 article [sw27254]
  • BASIS system for the simulation and storage of stochastic SBML models together with associated simulation ... services to allow users to incorporate its simulation tools into their workflows. Parameter inference ... formatting data) which addresses this problem for SBML models. It uses a sequential Bayesian MCMC...
  • SloppyCell

  • Referenced in 3 articles [sw13614]
  • SloppyCell is a software environment for simulation and analysis of biomolecular networks. Features: support ... Markup Language (SBML) level 2 version 3; deterministic and stochastic dynamical simulations; sensitivity analysis without...
  • yaml2sbml

  • Referenced in 1 article [sw38702]
  • YAML file into SBML for ODE simulation and into PEtab for parameter fitting. yaml2sbml offers...
  • MOCCASIN

  • Referenced in 2 articles [sw34252]
  • simulation models written in MATLAB or Octave and translate them into SBML format. It thereby...
  • peppercorn

  • Referenced in 1 article [sw33638]
  • results into SBML format for analysis in your favorite simulator. Note that the reaction rates...
  • JSim

  • Referenced in 4 articles [sw25988]
  • JSim is a Java-based simulation system for building quantitative numeric models and analyzing them ... also imports and exports model archive formats SBML and CellML...
  • httk

  • Referenced in 1 article [sw23160]
  • Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also ... PBTK” models to ”SBML” and ”JARNAC” for use with other simulation software. These functions...
  • Flint

  • Referenced in 1 article [sw34931]
  • simulator for biological and physiological models written in CellML, PHML, and/or SBML. Originally developed ... open, language-agnostic resource for reproducible simulation studies. While existing simultion tools, e.g. COPASI...