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libSBML-5.17.0

Keating, Sarah M; Bergmann, Frank; Olivier, Brett G; Smith, Lucian P; Hucka, Michael

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5.17.0 (2018-05-21)
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STABLE RELEASE

* Addition of support for the SBML Render package

  - Now that the first official version of the specification for the
    SBML Level 3 Rendering package is available, the libSBML API for
    'render' is now included in the stable release of libSBML.  This
    means that all prebuilt binaries for the stable release will
    include the 'render' package code. The src archive containing
    libSBML core code will continue to be available, with additional
    src archives available in the stable branch: one containing
    libSBML core plus all stable packages and additional archives of
    the individual package code.
    
    NOTE: The libSBML GNU make-based build system has not been updated
          for packages. Thus, to build from src, it is necessary to
          use the CMake build system.


* New features

  - The MATLAB language interface function TranslateSBML has been
    optimized for speed.

  - The MATLAB interface function OutputSBML can now be called with an
    output argument and no inputs; doing so will return information
    about the libSBML version and enabled packages used to build the
    binary files.

  - A new function getDefaultSBMLStruct has been added to the MATLAB
    interface. This function takes a string name of the element with
    level and version information and returns the relevant MATLAB-SBML
    structure for the element. Many thanks go to Thomas Pfau for
    supplying this function.

  - On occasion, the function getDerivedUnitDefinition that returns
    calculated units would report incorrect units without flagging any
    issues. This has been made less ambiguous and a derived
    UnitDefinition will not contain any units if it cannot be
    correctly determined.

  - Unit validation has been optimized and significantly speeded up for
    larger models. 
  
  - 'comp' package-specific updates:

    - The C API for comp has been completed.

  - 'fbc' package-specific updates:

    - SourceForge Tracker item #455: Error messages have been improved.
        
  - 'multi' package-specific updates:

    - The C API for multi has been completed.

  - 'qual' package-specific updates:

    - SourceForge Tracker item #455: Error messages have been improved.

  - 'render' package-specific updates:

    - A full C API for the render package has been added.

* Bug fixes

  - SourceForge Tracker item #459: An error in the function that
    converts libSBML infix notation to MATLAB infix notation failed
    when log functions failed. This is fixed. Thanks to Sven Thiele
    for reporting the issue.

  - The validation check for duplicate values of the 'metaid'
    attribute was not being extended to all packages. This has
    been fixed. 

  - Python examples have been updated to work with Python v3.

  - 'qual' package-specific bug fixes:

    - SourceForge Tracker item #457: Validation of rule qual-20311
      was producing an error when it should have been a warning.
      Thanks to Justin McManus for reporting the problem.


EXPERIMENTAL RELEASE

* New features

  - 'distrib' package-specific updates:

    - The 'distrib' package has undergone significant changes.
      The code has been fully updated to match this. We have also 
      used a Distrib prefix on all classes to prevent clashes with
      other packages or even other libraries. We welcome feedback 
      on this approach.

Files (27.7 MB)
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libSBML-5.17.0-Source.zip
md5:0a15c278893f1a5cf7f97ec21cd922ec
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  • Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008) LibSBML: An API Library for SBML. Bioinformatics, 24(6):880–881, doi:10.1093/bioinformatics/btn051.

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