January 10, 2022 Software Open Access

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

Dublin Core Export

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<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>Nicolas Rodriguez</dc:creator>
  <dc:creator>Andreas Dräger</dc:creator>
  <dc:creator>Mike Hucka</dc:creator>
  <dc:creator>David Emanuel Vetter</dc:creator>
  <dc:creator>Roman Schulte</dc:creator>
  <dc:creator>Bhavye Jain</dc:creator>
  <dc:creator>Christoph Blessing</dc:creator>
  <dc:creator>Leandro Watanabe</dc:creator>
  <dc:creator>tmHamm</dc:creator>
  <dc:creator>Onur101010</dc:creator>
  <dc:creator>Jakob Admard</dc:creator>
  <dc:creator>MeikeAi</dc:creator>
  <dc:creator>Ibrahim Vazirabad</dc:creator>
  <dc:creator>Alexander Dörr</dc:creator>
  <dc:creator>Piero Dalle Pezze</dc:creator>
  <dc:creator>Clemens82</dc:creator>
  <dc:creator>Lisa Falk</dc:creator>
  <dc:creator>marine3</dc:creator>
  <dc:creator>Wrzodek</dc:creator>
  <dc:creator>Alex Thomas</dc:creator>
  <dc:creator>thortiede</dc:creator>
  <dc:creator>RolandKeller5</dc:creator>
  <dc:creator>Florian Mittag</dc:creator>
  <dc:creator>Jan Rudolph</dc:creator>
  <dc:creator>Victor Kofia</dc:creator>
  <dc:creator>Tramy Nguyen</dc:creator>
  <dc:creator>Eugen Netz</dc:creator>
  <dc:creator>LeaBuchweitz</dc:creator>
  <dc:creator>Thomas Zajac</dc:creator>
  <dc:date>2022-01-10</dc:date>
  <dc:description>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:
  &lt;dependency&gt;
    &lt;groupId&gt;org.sbml.jsbml&lt;/groupId&gt;
    &lt;artifactId&gt;jsbml&lt;/artifactId&gt;
    &lt;version&gt;1.6.1&lt;/version&gt;
  &lt;/dependency&gt;

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</dc:description>
  <dc:identifier>https://zenodo.org/record/5833365</dc:identifier>
  <dc:identifier>10.5281/zenodo.5833365</dc:identifier>
  <dc:identifier>oai:zenodo.org:5833365</dc:identifier>
  <dc:relation>url:https://github.com/sbmlteam/jsbml/tree/jsbml-1.6.1</dc:relation>
  <dc:relation>doi:10.5281/zenodo.595308</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:title>sbmlteam/jsbml: JSBML 1.6.1</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
</oai_dc:dc>