{
  "version": "https://jsonfeed.org/version/1.1",
  "title": "chem-bla-ics",
  "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.",
  "home_page_url": "https://chem-bla-ics.linkedchemistry.info/",
  "feed_url": "https://chem-bla-ics.linkedchemistry.info/2025/03/16/CDK-UGM-2.json",
  "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png",
  "language": "en",
  "authors": [
    {
      "name": "Egon Willighagen",
      "url": "https://orcid.org/0000-0001-7542-0286",
      "_orcid": "0000-0001-7542-0286"
    }
  ],
  "items": [

    {
      "id": "https://doi.org/10.59350/n7e6r-p1e93",
      "url": "https://chem-bla-ics.linkedchemistry.info/2025/03/16/CDK-UGM-2.html",
      "title": "cdk2024 #5: Chemistry Development Kit User Group Meeting - Day 2",
      "content_html": "<p>Where <a href=\"https://chem-bla-ics.linkedchemistry.info/2025/03/11/CDK-UGM.html\">the first workshop day</a> had several\ntalks about new and old features of the <a href=\"https://cdk.github.io/\">Chemistry Development Kit</a> (CDK), the second day\nwas a hackathon day. We hacked and we talked. The coding was not mostly only the CDK repository itself,\nbut <a href=\"https://github.com/cdk/cdk/commits/main/?since=2025-03-10&amp;until=2025-03-11\">some things happened there</a> too:</p>\n\n<p><img src=\"/assets/images/cdk_hackathon.png\" alt=\"\" /></p>\n\n<p>Some pointers:</p>\n\n<ul>\n  <li>we worked on the <a href=\"http://cdk.github.io/cdkbook/\">Groovy Cheminformatics with the Chemistry Development Kit</a> book\n    <ul>\n      <li>move the repository to the GitHub organisation</li>\n      <li>improved the build system</li>\n    </ul>\n  </li>\n  <li>it was explored how the CDK can generate SMILES for glycans</li>\n  <li>continued work on updated tools using the CDK, e.g. <a href=\"https://apps.cytoscape.org/apps/chemviz2\">ChemViz2</a></li>\n  <li>code clean up, e.g. on <a href=\"https://github.com/cdk/cdk/commit/7263da00a86d97f965995bf7e706eadb95b90aa9\">JavaDoc</a>\nand <a href=\"https://github.com/cdk/cdk/commit/f8621e5fc02cfc73f52272b9dcc9354a4b0bc35d\">the XML parsing</a></li>\n  <li>a <a href=\"https://github.com/JChemPaint/jchempaint/releases/tag/3.4b\">JChemPaint release, based on CDK 2.10</a>,\nwith a <a href=\"https://flathub.org/apps/io.github.jchempaint.JChemPaint\">flatpak for easy install on many Linux distributions</a></li>\n</ul>\n\n<p>We further had discussions about a possible change of the license (what it would involve) and OSGi support.\nThe problem there is that Java packages can only exist in one OSGi bundle, and this is currently not the\ndiscuss. We discussed that the current modules were partially setup to clean up dependencies, and generally\nmodularize the CDK (e.g. each module could have a separate person responsible). We now want to propose\na larger <code class=\"language-plaintext highlighter-rouge\">core</code> module which covers the common cheminformatics functionality. A final discussion point\nI want to mention is that there are serious hints that we may have the Chemistry Development Kit\nas JavaScript in the browser soon!</p>\n\n<p>I like to thank every one who joined the workshop, particularly those that travelled to Maastricht\nfrom the UK, Germany, and Bulgaria. Also thanks to the six participants online who joined on the\nfirst day!</p>",
      "summary": "Where the first workshop day had several talks about new and old features of the Chemistry Development Kit (CDK), the second day was a hackathon day. We hacked and we talked. The coding was not mostly only the CDK repository itself, but some things happened there too:",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/cdk_hackathon.png",
      "date_published": "2025-03-16T00:00:00+00:00",
      "date_modified": "2025-03-16T00:00:00+00:00",
      "tags": ["cdk","openscience","cdk2024"],
      
      
      
      "_funding": [{"award": { "title" : "The Chemistry Development Kit in 2024: improving cheminformatics research", "acronym" : "CDK2024", "uri" : "drc.filenumber:osf232097" }, "funder": { "name": "Dutch Research Council", "ror": "04jsz6e67" } }],
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}