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libSBML R Example Programs

The libSBML 5.18.0 distribution comes with the following selection of complete example programs in the top-level file directory named examples/r.

Simple programs

  • echoSBML.R: Echos (and in the process, pretty prints) an SBML model.
  • readSBML.R: A simple command-line program that reads an SBML file and prints some statistics about it.
  • printSBML.R: Prints information about the top-level model in the given SBML file.
  • printSupported.R: Prints the supported SBML Levels and Versions for this copy of libSBML.

More advanced programs

  • addCVTerms.R: Adds controlled vocabulary terms to a species in a model.
  • convertSBML.R: Example demonstrating how to convert SBML documents between SBML Levels.
  • createExampleSBML.R: Lengthy example of creating SBML models presented in the SBML specification.
  • getAllElementsWithNotes.R: Demonstrates how to use the element filter class to search the model for elements with specific attributes .
  • printAnnotation.R: Prints the annotation strings for each element in a given model.
  • printMath.R: Prints the rule, reaction, and event formulas in a given SBML document.
  • printNotes.R: Prints the notes strings for each element in a given model.
  • printRegisteredPackages.R: A command-line program that prints the package plug-ins that are registered with this copy of libSBML.
  • printUnits.R: A command-line program that prints information about the units of measurement used in a given SBML file.
  • renameSId.R: Program that renames a specific SId and updates all references to it in a given model.
  • rngvalidator.R: Example of creating a RELAX NG (RNG) validator to be called during validation.
  • setIdFromNames.R: Program that renames all SIds that also have names specified. The new identifiers will be derived from the name, with all invalid characters removed.
  • setNamesFromIds.R: Program that changes all objects' "name" attribute values to match their "id" attribute values.
  • stripPackage.R: Strips the given SBML Level 3 package from the given SBML file.
  • translateL3Math.R: Translates infix formulas into MathML and vice-versa, using the SBML Level 3 parser instead of the old Level 1 parser.
  • unsetNotes.R: Unsets the notes for each element in the given SBML file.

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