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

DataCite XML Export

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  <identifier identifierType="DOI">10.5281/zenodo.5833365</identifier>
  <creators>
    <creator>
      <creatorName>Nicolas Rodriguez</creatorName>
      <affiliation>Babraham Institute, Cambridge, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Andreas Dräger</creatorName>
      <affiliation>Institute for Bioinformatics and Medical Informatics (IBMI)</affiliation>
    </creator>
    <creator>
      <creatorName>Mike Hucka</creatorName>
      <affiliation>California Institute of Technology</affiliation>
    </creator>
    <creator>
      <creatorName>David Emanuel Vetter</creatorName>
    </creator>
    <creator>
      <creatorName>Roman Schulte</creatorName>
    </creator>
    <creator>
      <creatorName>Bhavye Jain</creatorName>
      <affiliation>@sdsmdg</affiliation>
    </creator>
    <creator>
      <creatorName>Christoph Blessing</creatorName>
    </creator>
    <creator>
      <creatorName>Leandro Watanabe</creatorName>
    </creator>
    <creator>
      <creatorName>tmHamm</creatorName>
    </creator>
    <creator>
      <creatorName>Onur101010</creatorName>
    </creator>
    <creator>
      <creatorName>Jakob Admard</creatorName>
    </creator>
    <creator>
      <creatorName>MeikeAi</creatorName>
    </creator>
    <creator>
      <creatorName>Ibrahim Vazirabad</creatorName>
    </creator>
    <creator>
      <creatorName>Alexander Dörr</creatorName>
    </creator>
    <creator>
      <creatorName>Piero Dalle Pezze</creatorName>
      <affiliation>@Congenica</affiliation>
    </creator>
    <creator>
      <creatorName>Clemens82</creatorName>
    </creator>
    <creator>
      <creatorName>Lisa Falk</creatorName>
    </creator>
    <creator>
      <creatorName>marine3</creatorName>
    </creator>
    <creator>
      <creatorName>Wrzodek</creatorName>
    </creator>
    <creator>
      <creatorName>Alex Thomas</creatorName>
      <affiliation>C.H. Robinson</affiliation>
    </creator>
    <creator>
      <creatorName>thortiede</creatorName>
      <affiliation>@KohlbacherLab</affiliation>
    </creator>
    <creator>
      <creatorName>RolandKeller5</creatorName>
    </creator>
    <creator>
      <creatorName>Florian Mittag</creatorName>
    </creator>
    <creator>
      <creatorName>Jan Rudolph</creatorName>
      <affiliation>Phd student at MPI for Biochemistry</affiliation>
    </creator>
    <creator>
      <creatorName>Victor Kofia</creatorName>
    </creator>
    <creator>
      <creatorName>Tramy Nguyen</creatorName>
    </creator>
    <creator>
      <creatorName>Eugen Netz</creatorName>
    </creator>
    <creator>
      <creatorName>LeaBuchweitz</creatorName>
    </creator>
    <creator>
      <creatorName>Thomas Zajac</creatorName>
    </creator>
  </creators>
  <titles>
    <title>sbmlteam/jsbml: JSBML 1.6.1</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2022</publicationYear>
  <dates>
    <date dateType="Issued">2022-01-10</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/5833365</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/sbmlteam/jsbml/tree/jsbml-1.6.1</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.595308</relatedIdentifier>
  </relatedIdentifiers>
  <version>jsbml-1.6.1</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;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.&lt;/p&gt;
&lt;p&gt;To access this version of JSBML via Maven, please use:&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;  &amp;lt;dependency&amp;gt;
    &amp;lt;groupId&amp;gt;org.sbml.jsbml&amp;lt;/groupId&amp;gt;
    &amp;lt;artifactId&amp;gt;jsbml&amp;lt;/artifactId&amp;gt;
    &amp;lt;version&amp;gt;1.6.1&amp;lt;/version&amp;gt;
  &amp;lt;/dependency&amp;gt;
&lt;/code&gt;&lt;/pre&gt;
New Features
&lt;ul&gt;
&lt;li&gt;biojava-ontology was bumped to version 6.0.4.&lt;/li&gt;
&lt;li&gt;Convenient features, such as quick check for the presence of any specific &lt;code&gt;SBase&lt;/code&gt; extension&lt;/li&gt;
&lt;li&gt;Improvements to the documentation (JavaDoc, users' guide, and the project's &lt;code&gt;README&lt;/code&gt; file)&lt;/li&gt;
&lt;li&gt;Broader coverage of the offline validation capability&lt;/li&gt;
&lt;li&gt;Improved support for constraint-based modeling in the &lt;code&gt;ModelBuilder&lt;/code&gt;: automatic creation of common unit definition objects.&lt;/li&gt;
&lt;/ul&gt;
Bug Fixes
&lt;ul&gt;
&lt;li&gt;Update the dependency to log4j to version 2.17.0 after the announcement of a major security issue in the previous version.&lt;/li&gt;
&lt;li&gt;JSBML core does no longer have dependencies to any of the packages&lt;/li&gt;
&lt;li&gt;Preventing &lt;code&gt;ASTNode.astNodeToTree&lt;/code&gt; from recursive calls&lt;/li&gt;
&lt;li&gt;Correction of wrong comparisons with &lt;code&gt;==&lt;/code&gt; where &lt;code&gt;.equals()&lt;/code&gt; needs to be called for &lt;code&gt;String&lt;/code&gt; comparison&lt;/li&gt;
&lt;li&gt;Fixed Incorrect usage of model annotation&lt;/li&gt;
&lt;li&gt;Fixed return type of &lt;code&gt;createRenderCubicBezier&lt;/code&gt; method to &lt;code&gt;RenderCubicBezier&lt;/code&gt; Thanks to @eikept for this fix!&lt;/li&gt;
&lt;li&gt;Fixed incorrect unit derivation. Thanks to @eikept for this analysis!&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;When using JSBML, please cite:
☞ Rodriguez N., Thomas A., Watanabe L., Vazirabad I.Y., Kofia V. &lt;em&gt;et al&lt;/em&gt;. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics (2015), 31(20):3383–3386. &lt;a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtv341"&gt;https://doi.org/10.1093%2Fbioinformatics%2Fbtv341&lt;/a&gt;&lt;/p&gt;</description>
  </descriptions>
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