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@maxneal maxneal released this Jan 24, 2019 · 17 commits to master since this release

Differences between this version and previous (4.2.1)

  • includes a fix for reading in the RDF content of CellML models when there are multiple RDF blocks present
Assets 5

@maxneal maxneal released this Jan 8, 2019 · 20 commits to master since this release

Differences between this version and previous (4.2.0)

  • Fix for bug that was preventing some models from opening because of MathML elements not recognized by JSBML
  • Model classifier routine now looks at the XML content to determine model type for files with .xml extension
Assets 5

@maxneal maxneal released this Dec 28, 2018 · 25 commits to master since this release

Differences between this version and previous (4.1.0):

  • Support for specifying thermodynamic sources and sinks for force properties (fluid pressures, electrical potentials, etc.)
  • Users can search BioModels within a Project Tab and retrieve models from the repository
  • Users can now search and retrieve terms from UniProt for annotating proteins
  • Example models updated to indicate sources and sinks for force properties
  • Various bug fixes
  • Various enhancements to SemSim API codebase
Assets 5

@maxneal maxneal released this Sep 6, 2018 · 144 commits to master since this release

Differences between this version and previous (4.1.0 beta):

  • Support for SBML models that use Initial Assignments and Function Definitions
  • Reduced read/write times for SBML models
  • Various bug fixes and GUI enhancements
Assets 5

@maxneal maxneal released this Apr 10, 2018 · 239 commits to master since this release

Differences between this version and previous (4.0.0):

  • Provides basic read/write capabilities for OMEX archives

    • Model code and semantic annotations are stored in a separate files within the archive in accordance with COMBINE community recommendations (https://doi.org/10.1101/246470)
    • Currently SemGen only reads/writes one model per archive
  • Several bug fixes and enhancements

Assets 5

@maxneal maxneal released this Oct 5, 2017 · 354 commits to master since this release

Differences between this version and previous (4.0.0 alpha)

  • Project tab GUI enhancements and bug fixes
  • SemGen identifies rudimentary semantic similarity between biological concepts during merge
  • Bug fixes associated with reading and writing models in various formats
Assets 5

@maxneal maxneal released this Jun 23, 2017 · 504 commits to master since this release

Differences between this version and previous version 3.0.5:

  • Model composition (extraction and merging) is now accomplished using an integrated tool that uses D3-based network visualizations to display model content. Tool allows for extractions and merges to be performed within the same interface.
  • Original Merger and Extractor tools retired.
  • Many, many enhancements and bug fixes since the last version, hence the major version increment to 4.0.0.
Assets 5

@maxneal maxneal released this May 6, 2016 · 1172 commits to master since this release

Differences between this version and previous version 3.0.4:

  • Fixed bug that prevented loading CellML models
  • Users are no longer required to save extractions and mergers as SemSim OWL files before encoding in CellML or MML
  • Minor bug fixes and enhancements
Assets 5

@maxneal maxneal released this Mar 7, 2016 · 1212 commits to master since this release

Differences between this version and previous version 3.0.3:

  • If the Annotator cannot find the simulation source code as a local file, it now checks the directory in which the loaded model is stored
  • Reorganization of SemSim constants
  • Ontologies can be defined in a config file
  • Other minor bug fixes
Assets 5

@maxneal maxneal released this Feb 18, 2016 · 1226 commits to master since this release

Differences between this version and previous version 3.0.2:

  • SemGen now uses JSBML rather than libSBML native library bindings
  • Fixed bug that was causing the JSim API to delete SemGen.jar and README.txt on Linux distributions
  • Other minor bug fixes and enhancements
Assets 5
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