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

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{
  "description": "<p>This is a stable release of JSBML version 1.6.1. It comprises the two previously published snapshot releases, version 1.6 and version 1.6.1\u0251.</p>\n<p>To access this version of JSBML via Maven, please use:</p>\n<pre><code>  &lt;dependency&gt;\n    &lt;groupId&gt;org.sbml.jsbml&lt;/groupId&gt;\n    &lt;artifactId&gt;jsbml&lt;/artifactId&gt;\n    &lt;version&gt;1.6.1&lt;/version&gt;\n  &lt;/dependency&gt;\n</code></pre>\nNew Features\n<ul>\n<li>biojava-ontology was bumped to version 6.0.4.</li>\n<li>Convenient features, such as quick check for the presence of any specific <code>SBase</code> extension</li>\n<li>Improvements to the documentation (JavaDoc, users' guide, and the project's <code>README</code> file)</li>\n<li>Broader coverage of the offline validation capability</li>\n<li>Improved support for constraint-based modeling in the <code>ModelBuilder</code>: automatic creation of common unit definition objects.</li>\n</ul>\nBug Fixes\n<ul>\n<li>Update the dependency to log4j to version 2.17.0 after the announcement of a major security issue in the previous version.</li>\n<li>JSBML core does no longer have dependencies to any of the packages</li>\n<li>Preventing <code>ASTNode.astNodeToTree</code> from recursive calls</li>\n<li>Correction of wrong comparisons with <code>==</code> where <code>.equals()</code> needs to be called for <code>String</code> comparison</li>\n<li>Fixed Incorrect usage of model annotation</li>\n<li>Fixed return type of <code>createRenderCubicBezier</code> method to <code>RenderCubicBezier</code> Thanks to @eikept for this fix!</li>\n<li>Fixed incorrect unit derivation. Thanks to @eikept for this analysis!</li>\n</ul>\n<p>When using JSBML, please cite:\n\u261e Rodriguez N., Thomas A., Watanabe L., Vazirabad I.Y., Kofia V. <em>et al</em>. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics (2015), 31(20):3383\u20133386. <a href=\"https://doi.org/10.1093%2Fbioinformatics%2Fbtv341\">https://doi.org/10.1093%2Fbioinformatics%2Fbtv341</a></p>", 
  "license": "", 
  "creator": [
    {
      "affiliation": "Babraham Institute, Cambridge, UK", 
      "@type": "Person", 
      "name": "Nicolas Rodriguez"
    }, 
    {
      "affiliation": "Institute for Bioinformatics and Medical Informatics (IBMI)", 
      "@type": "Person", 
      "name": "Andreas Dr\u00e4ger"
    }, 
    {
      "affiliation": "California Institute of Technology", 
      "@type": "Person", 
      "name": "Mike Hucka"
    }, 
    {
      "@type": "Person", 
      "name": "David Emanuel Vetter"
    }, 
    {
      "@type": "Person", 
      "name": "Roman Schulte"
    }, 
    {
      "affiliation": "@sdsmdg", 
      "@type": "Person", 
      "name": "Bhavye Jain"
    }, 
    {
      "@type": "Person", 
      "name": "Christoph Blessing"
    }, 
    {
      "@type": "Person", 
      "name": "Leandro Watanabe"
    }, 
    {
      "@type": "Person", 
      "name": "tmHamm"
    }, 
    {
      "@type": "Person", 
      "name": "Onur101010"
    }, 
    {
      "@type": "Person", 
      "name": "Jakob Admard"
    }, 
    {
      "@type": "Person", 
      "name": "MeikeAi"
    }, 
    {
      "@type": "Person", 
      "name": "Ibrahim Vazirabad"
    }, 
    {
      "@type": "Person", 
      "name": "Alexander D\u00f6rr"
    }, 
    {
      "affiliation": "@Congenica", 
      "@type": "Person", 
      "name": "Piero Dalle Pezze"
    }, 
    {
      "@type": "Person", 
      "name": "Clemens82"
    }, 
    {
      "@type": "Person", 
      "name": "Lisa Falk"
    }, 
    {
      "@type": "Person", 
      "name": "marine3"
    }, 
    {
      "@type": "Person", 
      "name": "Wrzodek"
    }, 
    {
      "affiliation": "C.H. Robinson", 
      "@type": "Person", 
      "name": "Alex Thomas"
    }, 
    {
      "affiliation": "@KohlbacherLab", 
      "@type": "Person", 
      "name": "thortiede"
    }, 
    {
      "@type": "Person", 
      "name": "RolandKeller5"
    }, 
    {
      "@type": "Person", 
      "name": "Florian Mittag"
    }, 
    {
      "affiliation": "Phd student at MPI for Biochemistry", 
      "@type": "Person", 
      "name": "Jan Rudolph"
    }, 
    {
      "@type": "Person", 
      "name": "Victor Kofia"
    }, 
    {
      "@type": "Person", 
      "name": "Tramy Nguyen"
    }, 
    {
      "@type": "Person", 
      "name": "Eugen Netz"
    }, 
    {
      "@type": "Person", 
      "name": "LeaBuchweitz"
    }, 
    {
      "@type": "Person", 
      "name": "Thomas Zajac"
    }
  ], 
  "url": "https://zenodo.org/record/5833365", 
  "codeRepository": "https://github.com/sbmlteam/jsbml/tree/jsbml-1.6.1", 
  "datePublished": "2022-01-10", 
  "version": "jsbml-1.6.1", 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.5281/zenodo.5833365", 
  "@id": "https://doi.org/10.5281/zenodo.5833365", 
  "@type": "SoftwareSourceCode", 
  "name": "sbmlteam/jsbml: JSBML 1.6.1"
}