• COPASI

  • Referenced in 69 articles [sw12253]
  • alone program that supports models in the SBML standard and can simulate their behavior using...
  • BIOCHAM

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

  • Referenced in 22 articles [sw09942]
  • stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical ... parameter scan by an integration with SBML ODE Solver, SBML Simulation Core and Copasi ... CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate...
  • BioModels

  • Referenced in 32 articles [sw13610]
  • models can currently be retrieved in the SBML format, and import/export facilities are being developed...
  • sbtoolbox

  • Referenced in 18 articles [sw07391]
  • toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import ... export of SBML models. In this way the toolbox connects nicely to other SBML-enabled...
  • libSBML

  • Referenced in 13 articles [sw12937]
  • libSBML: An API library for SBML. Summary: LibSBML is an application programming interface library ... expressed in the Systems Biology Markup Language (SBML) format. It is written ... that facilitate adoption and use of both SBML and the library. Developers can embed libSBML ... themselves the work of implementing their own SBML parsing, manipulation and validation software...
  • SBML-SAT

  • Referenced in 7 articles [sw21897]
  • SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool. BACKGROUND ... biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding ... mathematical models of such processes. However, current SBML compatible software tools are limited in their ... work introduces a freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady...
  • Sbmltoolbox

  • Referenced in 6 articles [sw10558]
  • SBMLToolbox: an SBML toolbox for MATLAB users. We present SBMLToolbox, a toolbox that facilitates importing ... represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment ... that enables an experienced user of either SBML or MATLAB to combine the computing power ... with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions...
  • StochPy

  • Referenced in 7 articles [sw27252]
  • biology. It provides various stochastic simulation algorithms, SBML support, analyses of the probability distributions ... StochPy has been successfully tested against the SBML stochastic test suite, passing all tests. StochPy...
  • BiGG

  • Referenced in 10 articles [sw17247]
  • content, visualize metabolic pathway maps, and export SBML files of the models for further analysis...
  • SOSlib

  • Referenced in 5 articles [sw29331]
  • SOSlib (SBML ODE Solver Library): SOSlib is both a programming library and a command-line ... encoded in the Systems Biology Markup Language (SBML). It is written in ANSI/ISO ... multi-scale models with interfaces to non SBML data sources. Optional modules based on Graphviz...
  • ABC-SysBio

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

  • Referenced in 5 articles [sw35368]
  • Petri nets, can import all versions of SBML and can export SBML and MATLAB...
  • SimpleSBML

  • Referenced in 3 articles [sw34911]
  • Python package for creating, editing, and interrogating SBML models: Verison 2.0. In this technical report ... Python to more easily construct and inspect SBML based models. The most commonly used package ... constructing SBML models in Python is python-libSBML based on the C/C++ library libSBML. python ... create even the simplest models. Inspecting existing SBML models can also be difficult...
  • SBML Test Suite

  • Referenced in 3 articles [sw41895]
  • SBML Test Suite is a conformance testing system for SBML. It can be used ... test their software’s implementation of SBML support; it can also be used by modelers ... assess the correctness and completeness of SBML support in a given software system. The collection...
  • JSBML

  • Referenced in 3 articles [sw13871]
  • entirely Java-based library for working with SBML. The XML-based Systems Biology Markup Language ... SBML) is the de facto standard file format for the storage and exchange of biochemical ... provides many methods for manipulating and validating SBML files through its Application Programming Interface ... these reasons, several groups in the SBML community have mounted an open-source effort...
  • ProMoT

  • Referenced in 6 articles [sw02007]
  • model-exchange via the international standard SBML. Of specific importance for successful work in interdisciplinary...
  • SBML-PET

  • Referenced in 2 articles [sw12829]
  • SBML-PET: A systems biology markup language-based parameter estimation tool. Summary: The estimation ... present a Systems Biology Markup Language (SBML) based Parameter Estimation Tool (SBML-PET). The tool ... pathways, gene regulation networks and metabolic pathways. SBML-PET supports import and export ... models in the SBML format. It can estimate the parameters by fitting a variety...
  • SensSB

  • Referenced in 5 articles [sw19500]
  • Systems Biology Mark-up Language (SBML) format. Several examples from simple analytical functions to more...
  • Antimony

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