• COPASI

  • Referenced in 71 articles [sw12253]
  • stand-alone program that supports models in the SBML standard and can simulate their behavior...
  • Celldesigner

  • Referenced in 22 articles [sw09942]
  • Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory ... parameter scan by an integration with SBML ODE Solver, SBML Simulation Core and Copasi ... browse and modify existing SBML models with references to existing databases, simulate and view...
  • sbtoolbox

  • Referenced in 18 articles [sw07391]
  • interface for import and export of SBML models. In this way the toolbox connects nicely ... other SBML-enabled modelling packages. Models are represented in an internal model format...
  • BIOCHAM

  • Referenced in 45 articles [sw09927]
  • rule-based language for modeling biochemical systems (compatible with SBML); several simulators (boolean, differential, stochastic ... properties of a biological system and validate models with respect to such specifications, unique features...
  • SBML-SAT

  • Referenced in 7 articles [sw21897]
  • coding and sharing mathematical models of such processes. However, current SBML compatible software tools ... these models. RESULTS: This work introduces a freely downloadable, software package, SBML-SAT, which implements ... local and global sensitivity analysis for SBML models. This software tool extends current capabilities through ... tool for the analysis of their SBML models of biochemical and cellular processes...
  • BioModels

  • Referenced in 33 articles [sw13610]
  • they need. The models can currently be retrieved in the SBML format, and import/export facilities...
  • Sbmltoolbox

  • Referenced in 6 articles [sw10558]
  • SBMLToolbox: an SBML toolbox for MATLAB users. We present SBMLToolbox, a toolbox that facilitates ... importing and exporting models represented in the Systems Biology Markup Language (SBML ... portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML...
  • SimpleSBML

  • Referenced in 3 articles [sw34911]
  • package for creating, editing, and interrogating SBML models: Verison 2.0. In this technical report ... most commonly used package for constructing SBML models in Python is python-libSBML based ... even the simplest models. Inspecting existing SBML models can also be difficult ... that allows users to inspect existing SBML models without having to understand the underlying object...
  • BiGG

  • Referenced in 10 articles [sw17247]
  • metabolic pathway maps, and export SBML files of the models for further analysis by external...
  • PEtab

  • Referenced in 4 articles [sw36544]
  • reusability of the results of data-based modeling studies are essential. Yet, there has been ... problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value...
  • DOTcvpSB

  • Referenced in 4 articles [sw07305]
  • functional as possible. In systems biology, most models have a dynamic nature, usually consisting ... also contains a function for importing SBML models...
  • ABC-SysBio

  • Referenced in 8 articles [sw24739]
  • Systems Biology Markup Language (SBML). Deterministic and stochastic models can be analyzed in ABC-SysBio...
  • SBML-PET

  • Referenced in 2 articles [sw12829]
  • SBML-PET: A systems biology markup language-based parameter estimation tool. Summary: The estimation ... biological models including signaling pathways, gene regulation networks and metabolic pathways. SBML-PET supports ... import and export of the models in the SBML format. It can estimate the parameters ... supporting event definition in the SMBL model. SBML models can also be simulated in SBML...
  • CaliBayes

  • Referenced in 1 article [sw27254]
  • stochastic effects play an important role in models of human ageing, where ageing results from ... simulation and storage of stochastic SBML models together with associated simulation results. This system ... into their workflows. Parameter inference for stochastic models is also difficult and computationally expensive ... data) which addresses this problem for SBML models. It uses a sequential Bayesian MCMC method...
  • SOSlib

  • Referenced in 5 articles [sw29331]
  • encoded in the Systems Biology Markup Language (SBML). It is written in ANSI/ISO ... solvers or multi-scale models with interfaces to non SBML data sources. Optional modules based ... XMGrace allow a quick inspection of a model’s structure and dynamics. All functionalities...
  • JSim

  • Referenced in 4 articles [sw25988]
  • JSim also imports and exports model archive formats SBML and CellML...
  • ProMoT

  • Referenced in 6 articles [sw02007]
  • support for model-exchange via the international standard SBML. Of specific importance for successful work ... availability of graphical methods for model editing and exploration, because this defines a common language...
  • SBMLSim

  • Referenced in 1 article [sw41896]
  • abstraction layer for running simulations with SBML models in python and simplify common tasks occuring...
  • smfsbSBML

  • Referenced in 1 article [sw27069]
  • Stochastic modelling for systems biology. 3rd edition: Additional R package - smfsbSBML. There ... additional optional R Package for parsing SBML models into simulatable stochastic Petri net models...
  • Aeon

  • Referenced in 2 articles [sw42182]
  • open-source, fully compatible with SBML-qual models, and available as an online application with...