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Online SBML Validator Change Log

This change log summarizes changes made to the Online SBML Validator.

June 2018

  • Updated to accept a COMBINE Archive file and a PKZip file containing multiple files. Further information here.

May 2018

  • Bug fix: Potential crash when validating an SBML Level 2 file that also declared an SBML L3 package. This is not valid, but still should not crash. This is fixed.
  • Updated to latest release of libSBML (5.17.0)

March 2018

  • Update: The V1 recaptcha API is being retired by Google. We have updated to use the V2 API for unregistered users that would like to use the validaton of URLs.
  • Update: The error message relating to an incorrect unit on a <cn> element has been enhanced to provide more information.

February 2018

  • Bug fix: Duplicate values for the metaid attribute on package elements were not being reported. This is fixed.

January 2017

  • Unit checking code has been significantly optimized for speed.

December 2017

  • Updated to latest release of libSBML (5.16.0)

October 2017

  • Bug fix: An empty <fbc:geneProductAssociation/> element was causing a crash. This is now fixed and correctly reports the appropriate error.

August 2017

  • Bug fix: Line numbers for some 'comp' errors were incorrect. These have been improved.
  • Update and bug fix: The RNG schema for the 'spatial' packages has been fixed and updated to the latest specification.

June 2017

  • Bug fix: When validation code could not find an external reference it was entering an endless loop. This has been corrected.

May 2017

  • Clarification: When a file containing an unfinalized SBML L3 package is being used, some core validation may be disabled to avoid code failure. This meant a user may get an invalid file reported as valid. The validator now issues a warning, explaining the issue and suggesting the user re-runs validation with the option to 'Ignore unfinalized packages'.

April 2017

  • Updated to latest release of libSBML (5.15.0)

March 2017

  • Bug fix: A number of internal issues have been addressed. This has no impact on the user but facilitates internal diagnostics.

February 2017

  • Bug fix: A <stoichiometryMath> element with no child math element was causing a crash. This has been fixed.
  • Bug fix: A <functionDefinition> using math elements <pi/> or <exponentiale/> was failing to recognize these as numerical values and thus incorrectly reporting invalid math for elements requiring a numerical math value. This has been corrected.

December 2016

  • Updated RNG validation of the L3 'spatial' package to reflect latest specification changes.

September 2016

  • Bug fix: Validating units via the RESTful API was not working correctly. This has been fixed.
  • Updated to latest release of libSBML (5.14.0-experimental)

August 2016

  • replacement of the file upload by JavaScript only. This new system features also drag and drop operations.

May 2016

  • Bug fix: There was an anomaly between validating a compressed file containing layout and validating the uncompressed version. This was due to not catching defaults from SBML Level 2 in an SBML Level 3 model. This has been fixed.
  • The system now runs on faster back-end server hardware.

April 2016

  • Added an option in the validation output to send SBML FBCv2 models directly to the BiGG validator for additional types of analyses. This link is only shown if the model uploaded to the Online SBML Validator is an SBML FBCv2 model.
  • Updated to latest release of libSBML (5.13.0)

March 2016

  • The validator now supports validation of all SBML Level 3 packages for which specifications are available. For Level 3 packages that have been released in final form, validation is performed using the validation system integrated into libSBML; for Level 3 packages that are not in final form, validation is performed using a RELAX NG validation system and RELAX NG schemas for the packages.

February 2016

  • Bug fix: Validation was failing to catch when the <piece> element of a <piecewise> had an incorrect number of children.
  • SBO update: Since the validator uses a hard-coded snapshot of the SBO tree it is necessary to update the validator when new SBO terms are added.
  • Bug fix: Unit consistency checking was failing to interpret the units of <cn> elements when passed to a <functionDefinition>.
  • Bug fix: Unit consistency checking was failing to correctly deal with non-integer exponents.

December 2015

  • Bug fix: libSBML was failing to report that the variable attribute is not allowed on an <algebraicRule> element.

November 2015

  • Updated to latest release of libSBML (5.12.0)

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