{
  "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/2007/04/24/bioclipse-now-allows-qsar-descriptor.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/hs2p8-r1c84",
      "url": "https://chem-bla-ics.linkedchemistry.info/2007/04/24/bioclipse-now-allows-qsar-descriptor.html",
      "title": "Bioclipse now allows QSAR descriptor selection",
      "content_html": "<p>In preparation for the <a href=\"http://teacher.bmc.uu.se/BioclipseWS07/Welcome.html\">Embrace Workshop for Bioclipse</a> in May, I am working on the QSAR functionality of\n<a href=\"http://www.bioclipse.net/\">Bioclipse</a>. A nice extension point got set up some time ago, called\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2006/11/03/bioclipse-workshop-short-but.html\">DescriptorProvider <i class=\"fa-solid fa-recycle fa-xs\"></i></a>,\nand implemented by plugins to allow calculation of one or more descriptors for the selected molecules. Now, the\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2006/07/11/matrix-support-in-bioclipse.html\">functionality for the resulting matrix <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\nhas been around for some time too.</p>\n\n<p>What had not been available yet, was some GUI stuff to select descriptors to calculate, and the actual calculation. While the latter is yet to be\nhooked up, the selection of descriptors is now available:</p>\n\n<p><img src=\"/assets/images/bioclipseDescriptorSelection.png\" alt=\"\" /></p>\n\n<p>Interesting here is the use of OWL. CDK’s <code class=\"language-plaintext highlighter-rouge\">DescriptorEngine</code> provides a simple API written by Rajarshi that interfaces to the dictionary support\nfor OWL (which CDK offers in addition to CML based dictionaries). All CDK descriptors are written up in OWL (the\n<a href=\"http://cdk.svn.sourceforge.net/viewvc/cdk/trunk/cdk/src/org/openscience/cdk/dict/data/descriptor-algorithms.owl?view=markup\">source file</a>\nand the <a href=\"http://qsar.sourceforge.net/dicts/qsar-descriptors/index.xhtml\">HTML version</a>).\nYou’ll notice the weird characters in the screenshot; there something goes wrong with the encoding when reading the OWL.</p>",
      "summary": "In preparation for the Embrace Workshop for Bioclipse in May, I am working on the QSAR functionality of Bioclipse. A nice extension point got set up some time ago, called DescriptorProvider , and implemented by plugins to allow calculation of one or more descriptors for the selected molecules. Now, the functionality for the resulting matrix has been around for some time too.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/bioclipseDescriptorSelection.png",
      "date_published": "2007-04-24T00:00:00+00:00",
      "date_modified": "2025-04-12T00:00:00+00:00",
      
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}