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

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{
  "description": "<p>We are pleased to announce the release of JSBML-1.6, which is now available for download from GitHub and Maven.</p>\n<p>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.</p>\n<p>For more details, please visit the JSBML project home page:</p>\n<p><a href=\"http://sbml.org/Software/JSBML\">http://sbml.org/Software/JSBML</a></p>\nMajor new features\n<ul>\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 README file)</li>\n<li>Broader coverage of the offline validation capability</li>\n<li>Improved support for constraint-based modeling in the ModelBuilder: automatic creation of common unit definition objects.</li>\n</ul>\nBug fixes\n<ul>\n<li>Update the dependency to log4j to version xyz 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></li>\n<li>Fixed incorrect unit derivation</li>\n</ul>\n<p>Thank you for your interest and support of JSBML and SBML in general.</p>\n<p>When using JSBML, please cite</p>\n<ul>\n<li>N. Rodriguez <em>et al</em>. <a href=\"http://dx.doi.org/10.1093/bioinformatics/btv341\">JSBML 1.0: providing a smorgasbord of options to encode systems biology models</a>. Bioinformatics (2015), 31(20):3383\u20133386.</li>\n<li>A Dr\u00e4ger <em>et al</em>. <a href=\"https://doi.org/10.1093/bioinformatics/btr361\">JSBML: a flexible Java library for working with SBML</a>. Bioinformatics (2011), 27(15):2167\u20132168.</li>\n</ul>\nThe JSBML team.", 
  "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/5789493", 
  "codeRepository": "https://github.com/sbmlteam/jsbml/tree/v1.6", 
  "datePublished": "2021-12-17", 
  "version": "v1.6", 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.5281/zenodo.5789493", 
  "@id": "https://doi.org/10.5281/zenodo.5789493", 
  "@type": "SoftwareSourceCode", 
  "name": "sbmlteam/jsbml: JSBML 1.6"
}