December 17, 2021 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.5789493</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>
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    <creator>
      <creatorName>Bhavye Jain</creatorName>
      <affiliation>@sdsmdg</affiliation>
    </creator>
    <creator>
      <creatorName>Christoph Blessing</creatorName>
    </creator>
    <creator>
      <creatorName>Leandro Watanabe</creatorName>
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    <creator>
      <creatorName>tmHamm</creatorName>
    </creator>
    <creator>
      <creatorName>Onur101010</creatorName>
    </creator>
    <creator>
      <creatorName>Jakob Admard</creatorName>
    </creator>
    <creator>
      <creatorName>MeikeAi</creatorName>
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    <creator>
      <creatorName>Ibrahim Vazirabad</creatorName>
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    <creator>
      <creatorName>Alexander Dörr</creatorName>
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    <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</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <dates>
    <date dateType="Issued">2021-12-17</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/5789493</alternateIdentifier>
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  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/sbmlteam/jsbml/tree/v1.6</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.595308</relatedIdentifier>
  </relatedIdentifiers>
  <version>v1.6</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;We are pleased to announce the release of JSBML-1.6, which is now available for download from GitHub and Maven.&lt;/p&gt;
&lt;p&gt;JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.&lt;/p&gt;
&lt;p&gt;For more details, please visit the JSBML project home page:&lt;/p&gt;
&lt;p&gt;&lt;a href="http://sbml.org/Software/JSBML"&gt;http://sbml.org/Software/JSBML&lt;/a&gt;&lt;/p&gt;
Major new features
&lt;ul&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 README 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 ModelBuilder: 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 xyz 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;&lt;/li&gt;
&lt;li&gt;Fixed incorrect unit derivation&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;Thank you for your interest and support of JSBML and SBML in general.&lt;/p&gt;
&lt;p&gt;When using JSBML, please cite&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;N. Rodriguez &lt;em&gt;et al&lt;/em&gt;. &lt;a href="http://dx.doi.org/10.1093/bioinformatics/btv341"&gt;JSBML 1.0: providing a smorgasbord of options to encode systems biology models&lt;/a&gt;. Bioinformatics (2015), 31(20):3383–3386.&lt;/li&gt;
&lt;li&gt;A Dräger &lt;em&gt;et al&lt;/em&gt;. &lt;a href="https://doi.org/10.1093/bioinformatics/btr361"&gt;JSBML: a flexible Java library for working with SBML&lt;/a&gt;. Bioinformatics (2011), 27(15):2167–2168.&lt;/li&gt;
&lt;/ul&gt;
The JSBML team.</description>
  </descriptions>
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