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sbmlteam/jsbml: JSBML 1.6.1

Nicolas Rodriguez; Andreas Dräger; Mike Hucka; David Emanuel Vetter; Roman Schulte; Bhavye Jain; Christoph Blessing; Leandro Watanabe; tmHamm; Onur101010; Jakob Admard; MeikeAi; Ibrahim Vazirabad; Alexander Dörr; Piero Dalle Pezze; Clemens82; Lisa Falk; marine3; Wrzodek; Alex Thomas; thortiede; RolandKeller5; Florian Mittag; Jan Rudolph; Victor Kofia; Tramy Nguyen; Eugen Netz; LeaBuchweitz; Thomas Zajac

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

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