• Celldesigner

  • Referenced in 22 articles [sw09942]
  • stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical ... simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner supports simulation and parameter...
  • sbtoolbox

  • Referenced in 18 articles [sw07391]
  • purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface...
  • libSBML

  • Referenced in 13 articles [sw12937]
  • validating content expressed in the Systems Biology Markup Language (SBML) format. It is written...
  • SBML-SAT

  • Referenced in 7 articles [sw21897]
  • SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool. BACKGROUND ... analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known ... addition to its ability to handle systems with discontinuous events and intuitive graphical user interface...
  • ABC-SysBio

  • Referenced in 8 articles [sw24739]
  • work with models written in Systems Biology Markup Language (SBML). Deterministic and stochastic models...
  • Sbmltoolbox

  • Referenced in 6 articles [sw10558]
  • exporting models represented in the Systems Biology Markup Language (SBML...
  • SOSlib

  • Referenced in 5 articles [sw29331]
  • reaction network encoded in the Systems Biology Markup Language (SBML). It is written in ANSI/ISO ... Tree) for formula representation to construct ODE systems, their Jacobian matrix and other derivatives. CVODES...
  • PEtab

  • Referenced in 4 articles [sw36544]
  • parameter estimation problems using Systems Biology Markup Language (SBML) models...
  • PyBioNetFit

  • Referenced in 3 articles [sw34668]
  • modeling language (BNGL) or the Systems Biology Markup Language (SBML). PyBioNetFit offers a suite...
  • SloppyCell

  • Referenced in 3 articles [sw13614]
  • support for much of the Systems Biology Markup Language (SBML) level 2 version 3; deterministic...
  • JSBML

  • Referenced in 3 articles [sw13871]
  • with SBML. The XML-based Systems Biology Markup Language (SBML) is the de facto standard...
  • SBRML

  • Referenced in 3 articles [sw35191]
  • language for associating systems biology data with models. Results: We propose the Systems Biology Results ... Markup Language (SBRML), an XML-based language that associates a model with several datasets. Each...
  • SBML-PET

  • Referenced in 2 articles [sw12829]
  • SBML-PET: A systems biology markup language-based parameter estimation tool. Summary: The estimation ... major breakthrough in systems biology. We present a Systems Biology Markup Language (SBML) based Parameter ... designed to enable parameter estimation for biological models including signaling pathways, gene regulation networks ... solve the Ordinary Differential Equation (ODE) system...
  • SBMLsimulator

  • Referenced in 1 article [sw13435]
  • models encoded in the Systems Biology Markup Language (SBML). For simulation it contains the Systems...
  • BSTLab

  • Referenced in 1 article [sw33332]
  • models from SBML, the emerging Systems Biology Markup Language. https://bioinformatics.musc.edu/bstlab/...
  • LibSBMLSim

  • Referenced in 1 article [sw41444]
  • functional SBML simulator. Motivation: The Systems Biology Markup Language (SBML) is currently supported ... within this field, there is still no language-neutral library that supports all features ... development of a computational platform for systems biology. Results: We implemented a library called libSBMLSim...
  • SuBliMinaL

  • Referenced in 1 article [sw27602]
  • modules manipulate reconstructions encoded in Systems Biology Markup Language (SBML), and can be chained...
  • SBMLDiagrams

  • Referenced in 1 article [sw41894]
  • SBML layout and render. The Systems Biology Markup Language (SBML) is an extensible standard format...
  • MASSpy

  • Referenced in 1 article [sw41441]
  • implementation of libRoadRunner: the Systems Biology Markup Language (SBML) simulation engine. Three examples are provided...
  • PubChem PUG

  • Referenced in 1 article [sw36343]
  • information resource for the chemical biology research community, it routinely receives more than 1 million ... data is provided by several different systems, including the US National Center for Biotechnology Information ... that exchanges data through eXtended Markup Language (XML). Further simplifying programmatic access, PubChem provides...