{
  "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/2007/06/27/qsar-plugin-for-bioclipse-getting-in.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/ht8k2-aed07",
      "url": "https://chem-bla-ics.linkedchemistry.info/2007/06/27/qsar-plugin-for-bioclipse-getting-in.html",
      "title": "QSAR plugin for Bioclipse getting in shape",
      "content_html": "<p>Over the last few weeks I continued the work on getting (descriptor-based) <a href=\"http://en.wikipedia.org/wiki/QSAR\">QSAR</a>/QSPR implemented in\n<a href=\"http://www.bioclipse.net/\">Bioclipse</a>. <a href=\"http://joelib.sf.net/\">JOELib</a> (GPL) and the <a href=\"http://cdk.sf.net/\">CDK</a> (LGPL) being two prominent\nopensource engines that can calculate molecular descriptors, and <a href=\"http://ambit.acad.bg/\">AMBIT</a> a front-end.</p>\n\n<p>To be able to do QSAR/QSPR model building from start to end in Bioclipse, I worked in April\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2007/04/24/bioclipse-now-allows-qsar-descriptor.html\">on an architecture for selecting descriptors <i class=\"fa-solid fa-recycle fa-xs\"></i></a>.\nBeing busy with so many things, it took me some time to get around to completing that, but here are the screenshots:</p>\n\n<p><img src=\"/assets/images/bioQSAR1.png\" alt=\"\" /></p>\n\n<p>The funny characters and the whitespace is gone. Right now, it still only lists one provider, but I plan to add JOELib plugin soon.\nThe list of actual descriptors is provided by the extension.</p>\n\n<p>What Bioclipse then does, is have the extension calculate the descriptor values for the selected <code class=\"language-plaintext highlighter-rouge\">CDKResource</code> in the BioNavigator\nusing the selected descriptors. This will then create a new <code class=\"language-plaintext highlighter-rouge\">MatrixResource</code> in the Bioclipse workspace (currently called\nqsarResult.jam), and which is opened in the Matrix editor:</p>\n\n<p><img src=\"/assets/images/bioQSAR1.png\" alt=\"\" /></p>\n\n<p>There is still enough work left to do. For example, the columns are not yet labeled according to the descriptor name, and\nselecting more than one <code class=\"language-plaintext highlighter-rouge\">CDKResource</code> in the navigator does not give a multirow matrix yet.</p>",
      "summary": "Over the last few weeks I continued the work on getting (descriptor-based) QSAR/QSPR implemented in Bioclipse. JOELib (GPL) and the CDK (LGPL) being two prominent opensource engines that can calculate molecular descriptors, and AMBIT a front-end.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/bioQSAR.png",
      "date_published": "2007-06-27T00:00:00+00:00",
      "date_modified": "2025-08-10T00:00:00+00:00",
      "tags": ["bioclipse","qsar","cdk","ambit"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}