Changes in MathSBML version 2.5

Version 2.5.0 release date: 1 June 2005 (superceded - see release notes for a list of releases).

Version 2.4.0 release date: 24 September 2004 (previous release).

This page summarizes the changes in MathSBML that have been implemented since the release of version 2.4.0 through version 2.5.0, including all cvs'd versions 2.4.X. To see the changes that were implemented in version 2.4.0 since the release of version 2.3.0 click here.

To see a summary of changes in earlier release, click here.

To see a summary of known issues and bugs, click here.

To provide feedback, click here.

• Major changes
  • Full support for SBML Level 2 version 2
  • Full simulation support for models with events, including delays
  • Compatible with Mathematica versions through 5.1.1
  • Support multi-compartment models

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• Model Builder
  • Full support for SBML Level 2 version 2
    • Nested Units
    • Constraint Rules
  • Check for shadowing of global variables by local reaction parameters.
  • Check for (and don't allow) global identifier collision.
  • Correct implementation of units fields as per SBML errata: Corrected formula is unew=(multiplier×10^scale×u)^exponent+offset
  • addSpecies adds species to most recently defined compartment rather than first compartment in the model.
  • Allow kinetic law to be specified as a text string as well as an expression (in addReaction).
  • New functions:
    • getX where X=compartment,function, parameter, species, speciesType, reaction, rule, unit to retrieve an object by either name or number in symbolic SBML.
    • getXs where X=compartment,function, parameter, species, speciesType, reaction, rule, unit to retrieve a list of all the objects of that type in symbolic SBML.
    • getNumberOfX where X=compartment,function, parameter, species, speciesType, reaction, rule, unit to obtain the number of the specified type of object.
    • getModel to retrieve the current full model in symbolicSBML (alias for createSymbolicModel).
    • getObject[X,list] where X=compartment,function, parameter, species, speciesType, reaction, rule, unit and list is a list of integers and/or ids.

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• SBML Read
  • List of options returned is alphabetized
  • New and changed options returned (all are optional)
    • SBMLConstants - NEW: returns all globally defined constants in the model, what was previously returned by SBMLParameters.
    • SBMLLeveVersion - NEW: returns a real number such as 2.2 indicating level.version
    • SBMLMassBalanceEquations - NEW: returns mass balance odes based on the stoichiometry matrix in the model.
    • SBMLMassActionEquations - NEW: returns mass action equations based on the stoichiometry matrix in the model.
    • SBMLModelVariables - NEW: list of all variables in the model, previously returned as SBMLSpecies.
    • SBMLParameters- MODIFIED: now only returns global parameters, not all globally defined constants in the model.
    • SBMLSpecies - MODIFIED: now only returns species, not all variables in the model.
    • SBMLStoichiometryMatrix - NEW: returns stoichiometry matrix based on stoichiometries specified in the model reactions.
  • Verbose listing (also applies to SBMLWrite html format.
    • New section lists speciesTypes (Level.Version ≥ 2.2 only).
    • New column in species listing displays speciesTypes (Level.Version ≥ 2.2 only)
    • If units on a species "cancel" they are displayed as "dimensionless" rather than "1"
    • Exponents displayed as x^y rather than mathematica format x*^y
    • Display creation and annihilation reactions as "→x+y+..." or "U+V+...→" instead of "EmptySet→x+y+...", etc.
  • Check for shadowing of global variables by local reaction parameters
  • Check for global identifier collision (print error message)

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• SBMLNDSolve
  • Support for SBML Level 2 Version 2
    • Print message when constraintRule is violated.
  • Full support for events, including the delay field, in Level 2
  • Stricter adherence to spec during simulations
    • All initial conditions and parameter values must be specified, defaults are no longer provided, including compartment volumes.
  • Bug Fixes
    • Fix bug where some level 1 models would not be solved.

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• SBMLPlot
  • Bug Fixes
    • Allow SBMLGridPlot works on models with events
    • Fix bug where some models without events would not be plotted
    • Fix bug in log plots where some level 1 models would not be plotted
    • Improved log plots, check for zero/negative values and ignore those points but still plot rest of the data (and print message indicating that some data was not plotted)

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• General Changes
  • Supports simulation of models with events
  • Bug Fixes
    • Corrected support for mathml piecewise
    • Corrected support for annotations: as <foo:x="y"> when foo is known.
  • Compatible with Mathematica versions through 5.1.1
  • Less reliance on default values in simulation - stricter adherence to spec.
  • ODEs that are generated support mult-compartment models by taking compartment volumes into account.

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