MathSBML

MathSBML Release Notes

This page summarizes some of the key changes in various releases of MathSBML.

Compatibility Matrix

Mathematica Version	MathSBML Version
6.0.1	2.7.4 (Verified in Linux 2.7.22; Mac OSX/10.4; Win/XP)
6.0.0	Not Supported: Please upgrade to 6.0.1 (The XML libraries in 6.0.0 do not work correctly!)
5.2	2.7.4
5.1	2.7.4
Versions we unable to support:
5.0	2.6.1 (2.7++ is incompatible)
4.2	2.6.1
< 4.2	Not Tested

File Releases

Version 2.7.x(cvs only)

SBMLNDSolve: Apply initial assignments to constant size compartments (1887544)
SBMLPlot: Fix bug in which all variables are sometimes plotted even when only a subset are requested (1892066)
SBMLRead, model builder: timeUnit and substanceUnit are disallowed in L2V3 kinetic laws
SBMLRead, model builder: fix a bug in stoichiometryMath (1889895)
resetIC: fix bug that caused crasheds in M6 (1891204)
Install scripts for linux and mac added

Version 2.7.1, released 7 Dec 2007
- In SBMLNDSolve, compartments with unspecified sizes default to 1
- New Function getBiomodel reads directly from the online Biomodels database.
- Fix some bugs in handling e-format and email addresses.
- Fix clipping of some variables in SBMLPlot when multiple variables are plotted together
- Improve handling of variables that duplicate System names.
Version 2.7, released 29 August 2007
- Mathematica 6.0 Compatibility
- SBML Level 2 Version 3
- SBMLValidator function is moved to a separate plugin
- New functions getObjectAttribute, getObjectID, getObjectName, getObjectNames
- New functions getXID, getXName, getXIDs, getXNames where X = species, compartment, ...
- New options "annotations", "notes", "comments" in createModel[] to suppress any of these attributes at the topmost level.
Version 2.6.1a, released 24 April 2007
- New field in SBMLRead: SBMLBoundaryConditions
- new functions parametricScan
- new function icScan
- new function visiualizeSBMLModel
- new plugin for layout.m
- new plugin for Inverse Eigenvalue Analysis
- Fix bugs in multicompartmental model simulation
- Fix several bugs in plotting through events.
Version 2.6, released 01 October 2006
- Support for SBML Level 2 Version 2, including:
  - initialAssignments (SBMLRead, SBMLNDSolve, Model Builder)
  - constraints (SBMLRead, SBMLNDSolve, Model Builder)
  - speciesType (SBMLRead, Model Builder)
  - compartmentType (SBMLRead, Model Builder)
  - tracking of SBOTerms (SBMLRead)
  - MIRIAM creator object (Model Builder)
  - Ability to plot kinetic law via reaction id (SBMLNDSolve, SBMLRead, SBMLPlot)
- Support for all types of csymbol
- Ability to add csymbol to any math expression in model builder
- Ability to specify an absolute path name (SBMLRead)
- Ability to use online SBML model validator from within Mathematica
- Strict type checking in elements
- Improved handling of e-format
- new functions resetIC, resetParameter can change values of IC or a parameter after it has been loaded into the simulator: no need to rebuild and reload the SBML model
- conservationMatrix can be returned by SBMLRead
- getXNumber[id], replaceX for any object X (Model Builder)
- options PlotStyles and holdLegend (SBMLPlot)
- Significantly improved model validation and error messages
  - check for identifier collision
  - check for undefined identifiers in all math expressions
  - correct use of functions
  - check for use of proper subset of MathML
  - checks for previous load of MathSBML or conflicting version load
- Various bug fixes
Version 2.5 release date: 1 June 2005. Click for Detailed Release Notes
- Support for SBML Level 2 Version 2 Proposals from Heidelberg
- Simulation of models with event delays
- Multi-compartment models
- Stoichiometry matrix and mass-action or mass-balance equations
- new functions getObject
- Fix bugs reported through Tokyo Hackathon
Version 2.4 release date: 24 September 2004. Click for Detailed Release Notes.
- Support for csymbol time
- Enforce correct rule ordering
- Support units of the species
- html style sheets
- Berkeley Madonna output
- DAE support (requires Mathematica 4.2++)
- Improved annotation support
- Heidelberg Forum pre-release
Version 2.3 release date: 15 March 2004.
- Simulation of models with events
- Model builder support for metaid, notes & annotations
- Computable Plant Array Proposal
- Hinxton Hackathon pre-release
Version 2.2 release date: 17 October 2003.
- First release of Model Builder
- St. Louis Forum pre-release
Version 2.1 release date: 7 August 2003.
- Include all level 1 predefined rate laws
- Output support to XPP, HTML, Fortran
- Fix bugs reported through Virginia Hackathon
Version 2.0 release date: 30 June 2003.

Support for SBML Level 2

Version 1.0 release date: 3 April 2003
- Initial release

This page was last revised on 12 April 2008.