Table of Contents
The following are example programs demonstrating the use of different libSBML API calls. The programs are available in different programming languages. (Due to limited resources, not all programs are available in all programming languages supported by libSBML.) Further below, you can also find examples of using SBML Level 3 packages.
Simple programs
| Name | Description | C | C++ | C# | Java | JS | Perl | PHP | Python | R | Ruby |
|---|---|---|---|---|---|---|---|---|---|---|---|
| echoSBML | Echoes (and in the process, pretty prints) an SBML model. | — | — | — | — | — | — | — | — | — | — |
| readSBML | A simple command-line program that reads an SBML file and prints some statistics about it. | — | — | — | — | — | — | — | — | — | — |
| printSBML | Prints information about the top-level model in the given SBML file. | — | — | — | — | — | — | — | — | — | — |
| printSupported | Prints the supported SBML Levels and Versions for this copy of libSBML. | — | — | — | — | — | — | — | — | — | — |
| printRegisteredPackages | Prints the SBML Level 3 packages registered/installed in this copy of libSBML. | — | — | — | — | — | — | — | — | — | — |
More advanced programs
| Name | Description | C | C++ | C# | Java | JS | Perl | PHP | Python | R | Ruby |
|---|---|---|---|---|---|---|---|---|---|---|---|
| addCVTerms | Adds controlled vocabulary terms to a species in a model. | — | — | — | — | — | — | — | — | — | — |
| addCustomValidator | Example of creating a custom validator to be called during validation. | — | — | — | — | — | — | — | — | — | — |
| addModelHistory | Adds a model history to a model. | — | — | — | — | — | — | — | — | — | — |
| addingEvidenceCodes_1 | Adds controlled vocabulary terms to a reaction in a model. | — | — | — | — | — | — | — | — | — | — |
| addingEvidenceCodes_2 | Adds evidence codes to a species in a model. | — | — | — | — | — | — | — | — | — | — |
| appendAnnotation | Adds annotation strings to a model and a species. | — | — | — | — | — | — | — | — | — | — |
| callExternalValidator | Example that shows how to call an external program for validation. | — | — | — | — | — | — | — | — | — | — |
| convertSBML | Example demonstrating how to convert SBML documents between SBML Levels. | — | — | — | — | — | — | — | — | — | — |
| createExampleSBML | Lengthy example of creating SBML models presented in the SBML specification. | — | — | — | — | — | — | — | — | — | — |
| getAllElementsWithNotes | Demonstrates how to use the element filter class to search the model for elements with specific attributes . | — | — | — | — | — | — | — | — | — | — |
| inlineFunctionDefintions | Loads an SBML File and inlines all the function definitions found in the model. | — | — | — | — | — | — | — | — | — | — |
| printAnnotation | Prints the annotation strings for each element in a given model. | — | — | — | — | — | — | — | — | — | — |
| printMath | Prints the rule, reaction, and event formulas in a given SBML document. | — | — | — | — | — | — | — | — | — | — |
| printNotes | Prints the notes strings for each element in a given model. | — | — | — | — | — | — | — | — | — | — |
| printRegisteredPackages | A command-line program that prints the package plug-ins that are registered with this copy of libSBML. | — | — | — | — | — | — | — | — | — | — |
| printUnits | A command-line program that prints information about the units of measurement used in a given SBML file. | — | — | — | — | — | — | — | — | — | — |
| promoteParameters | Promote all local parameters in the model to global parameters. | — | — | — | — | — | — | — | — | — | — |
| renameSId | Program that renames a specific SId and updates all references to it in a given model. | — | — | — | — | — | — | — | — | — | — |
| rngvalidator | Example of creating a RELAX NG (RNG) validator to be called during validation. | — | — | — | — | — | — | — | — | — | — |
| setIdFromNames | 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 | Program that changes all objects name attribute values to match their id attribute values. | — | — | — | — | — | — | — | — | — | — |
| stripPackage | Strips the given SBML Level 3 package from the given SBML file. | — | — | — | — | — | — | — | — | — | — |
| translateL3Math | Translates infix formulas into MathML and vice-versa, using the SBML Level 3 parser instead of the old Level 1 parser. | — | — | — | — | — | — | — | — | — | — |
| translateMath | Translates infix formulas into MathML and vice-versa. | — | — | — | — | — | — | — | — | — | — |
| unsetAnnotation | Unsets the annotation for each element in the given SBML file. | — | — | — | — | — | — | — | — | — | — |
| unsetNotes | Unsets the notes for each element in the given SBML file. | — | — | — | — | — | — | — | — | — | — |
| validateSBML | Validates one or more SBML files. | — | — | — | — | — | — | — | — | — | — |
Programs using SBML Level 3 packages
The libSBML API documentation has examples programs using libSBML plug-ins that support SBML Level 3 packages. Please consult the appropriate libSBML API documentation for your programming language.