• LibSBMLSim

  • Referenced in 1 article [sw41444]
  • simulator. Motivation: The Systems Biology Markup Language (SBML) is currently supported by >230 software tools ... integration of ordinary differential equation (ODE) models. Although SBML is a widely accepted standard within ... 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...
  • MOCCASIN

  • Referenced in 2 articles [sw34252]
  • MOCCASIN stands for ”Model ODE Converter for Creating Automated SBML INteroperability”. MOCCASIN is designed ... them into SBML format. It thereby enables researchers to convert MATLAB models into an open...
  • Antimony

  • Referenced in 5 articles [sw34912]
  • packages to import these models and convert them either to SBML or their own internal...
  • StochPy

  • Referenced in 7 articles [sw27252]
  • experienced user. Here we present StochPy (Stochastic modeling in Python), which is a flexible software ... biology. It provides various stochastic simulation algorithms, SBML support, analyses of the probability distributions ... illustrate the functionality of StochPy with stochastic models of gene expression, cell division, and single ... StochPy has been successfully tested against the SBML stochastic test suite, passing all tests. StochPy...
  • SBML Test Suite

  • Referenced in 3 articles [sw41895]
  • implementation of SBML support; it can also be used by modelers to assess the correctness...
  • MathSBML

  • Referenced in 0 articles [sw06795]
  • open-source package for working with SBML models in Mathematica. It provides facilities for reading ... SBML models, converting them to systems of ordinary differential equations for simulation and plotting ... models to other formats. It supports both Level 1 and Level 2 SBML...
  • Path2Models

  • Referenced in 4 articles [sw29332]
  • constraint-based. Models from over 2 600 organisms are encoded consistently in SBML...
  • SBML-shorthand

  • Referenced in 1 article [sw27071]
  • tool that translates the shorthand model description to real SBML. It isn’t really meant ... essential model structure. Once the basics are defined, you can translate to SBML and load...
  • BSTLab

  • Referenced in 1 article [sw33332]
  • functions needed to reformulate and transport models from SBML, the emerging Systems Biology Markup Language...
  • httk

  • Referenced in 1 article [sw23160]
  • also provided for exporting ”PBTK” models to ”SBML” and ”JARNAC” for use with other simulation...
  • SensSB

  • Referenced in 5 articles [sw19500]
  • able to import models in the Systems Biology Mark-up Language (SBML) format. Several examples ... quantified by increased identifiability metrics of the models and decreased confidence intervals of the estimated...
  • SBMLDiagrams

  • Referenced in 1 article [sw41894]
  • format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout ... This allows modelers to describe a biochemical model as a pathway diagram. However ... easily add and retrieve such information from SBML. In this application note we describe...
  • SBMLsimulator

  • Referenced in 1 article [sw13435]
  • SBML. SBMLsimulator is a fast, accurate, and easily usable program for dynamic model simulation ... parameter optimization of models encoded in the Systems Biology Markup Language (SBML). For simulation ... benchmarked against the entire SBML Test Suite and all models from the Biomodels.net database. SBMLsimulator...
  • Cyto-Sim

  • Referenced in 5 articles [sw35368]
  • currently supports models described as Petri nets, can import all versions of SBML...
  • PyBioNetFit

  • Referenced in 3 articles [sw34668]
  • rule-based modeling language (BNGL) or the Systems Biology Markup Language (SBML). PyBioNetFit offers ... search) for parameter optimization. In addition to model parameterization, PyBNF supports uncertainty quantification by bootstrapping...
  • GillesPy2

  • Referenced in 2 articles [sw38638]
  • Cython, and NumPy. Models can also be read from files in SBML format...
  • SBML2Julia

  • Referenced in 1 article [sw36528]
  • SBML2Julia: interfacing SBML with efficient nonlinear Julia modelling and solution tools for parameter optimization. Motivation ... optimization time of a microbial community model by a factor of 140. To facilitate access ... SBML2Julia. SBML2Julia translates optimisation problems specified in SBML and TSV files (PEtab format) into Julia...
  • BioLQM

  • Referenced in 2 articles [sw35162]
  • logical models, bioLQM implements import and export facilities, notably for the recent SBML qual exchange ... design of workflows combining these tools. Model modifications enable the definition of various perturbations...
  • yaml2sbml

  • Referenced in 1 article [sw38702]
  • convert an ODE model specified in a YAML file into SBML for ODE simulation ... fitting. yaml2sbml offers: a translator of ODE models specified in YAML into SBML/PEtab...
  • Biosimware

  • Referenced in 1 article [sw01324]
  • dynamics of single or multi-volume models, as well as automatic tools to analyze ... parameters. BioSimWare supports SBML format, and can automatically convert stochastic models into the corresponding deterministic...