JSBML 1.6.1

This is a stable release of JSBML version 1.6.1. It comprises the two previously published snapshot releases, version 1.6 and version 1.6.1ɑ.

To access this version of JSBML via Maven, please use:

  <dependency>
    <groupId>org.sbml.jsbml</groupId>
    <artifactId>jsbml</artifactId>
    <version>1.6.1</version>
  </dependency>

New Features

• biojava-ontology was bumped to version 6.0.4.
• Convenient features, such as quick check for the presence of any specific SBase extension
• Improvements to the documentation (JavaDoc, users' guide, and the project's README file)
• Broader coverage of the offline validation capability
• Improved support for constraint-based modeling in the ModelBuilder: automatic creation of common unit definition objects.

Bug Fixes

• Update the dependency to log4j to version 2.17.0 after the announcement of a major security issue in the previous version.
• JSBML core does no longer have dependencies to any of the packages
• Preventing ASTNode.astNodeToTree from recursive calls
• Correction of wrong comparisons with == where .equals() needs to be called for String comparison
• Fixed Incorrect usage of model annotation
• Fixed return type of createRenderCubicBezier method to RenderCubicBezier Thanks to @eikept for this fix!
• Fixed incorrect unit derivation. Thanks to @eikept for this analysis!

When using JSBML, please cite:
☞ Rodriguez N., Thomas A., Watanabe L., Vazirabad I.Y., Kofia V. et al. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics (2015), 31(20):3383–3386. https://doi.org/10.1093%2Fbioinformatics%2Fbtv341