{
  "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/2010/08/04/using-bioclipse-to-upload-data-to.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/f0s4t-znm21",
      "url": "https://chem-bla-ics.linkedchemistry.info/2010/08/04/using-bioclipse-to-upload-data-to.html",
      "title": "Using Bioclipse to upload data to an OpenTox server",
      "content_html": "<p>As part of a continuing mashup of <a href=\"http://www.bioclipse.net/\">Bioclipse</a> and <a href=\"http://www.opentox.org/\">OpenTox</a>, I sat down with Nina in\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2010/08/01/oxford.html\">Oxford <i class=\"fa-solid fa-recycle fa-xs\"></i></a> to implement uploading molecules from within Bioclipse with JavaScript to\nOpenTox servers. This opens the route to calculate QSAR descriptors using the\n<a href=\"http://opentox.org/dev/apis/api-1.1/\">OpenTox API</a>.</p>\n\n<p>As, a result, you can (with the code at my laptop) now do (see this <a href=\"http://www.myexperiment.org/workflows/1468\">BSL script at MyExperiment</a>):</p>\n\n<div class=\"language-javascript highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"c1\">// requires an unspecified Bioclipse development version</span>\n\n<span class=\"nx\">ds</span> <span class=\"o\">=</span> <span class=\"nx\">opentox</span><span class=\"p\">.</span><span class=\"nf\">createDataset</span><span class=\"p\">(</span><span class=\"dl\">\"</span><span class=\"s2\">http://apps.ideaconsult.net:8080/ambit2/</span><span class=\"dl\">\"</span><span class=\"p\">);</span>\n\n<span class=\"nx\">opentox</span><span class=\"p\">.</span><span class=\"nf\">addMolecule</span><span class=\"p\">(</span><span class=\"nx\">ds</span><span class=\"p\">,</span> <span class=\"nx\">cdk</span><span class=\"p\">.</span><span class=\"nf\">fromSMILES</span><span class=\"p\">(</span><span class=\"dl\">\"</span><span class=\"s2\">CCCCC[N+](C)(C)C</span><span class=\"dl\">\"</span><span class=\"p\">))</span>\n<span class=\"nx\">opentox</span><span class=\"p\">.</span><span class=\"nf\">addMolecule</span><span class=\"p\">(</span><span class=\"nx\">ds</span><span class=\"p\">,</span> <span class=\"nx\">cdk</span><span class=\"p\">.</span><span class=\"nf\">fromSMILES</span><span class=\"p\">(</span><span class=\"dl\">\"</span><span class=\"s2\">ClC(I)Br</span><span class=\"dl\">\"</span><span class=\"p\">))</span>\n\n<span class=\"nx\">opentox</span><span class=\"p\">.</span><span class=\"nf\">deletaDataset</span><span class=\"p\">(</span><span class=\"nx\">ds</span><span class=\"p\">);</span>\n</code></pre></div></div>\n\n<p>Make sure to check out the other stuff <a href=\"http://chem-bla-ics.blogspot.com/search?q=opentox\">I have been doing with respect to OpenTox</a>.</p>",
      "summary": "As part of a continuing mashup of Bioclipse and OpenTox, I sat down with Nina in Oxford to implement uploading molecules from within Bioclipse with JavaScript to OpenTox servers. This opens the route to calculate QSAR descriptors using the OpenTox API.",
      
      "date_published": "2010-08-04T00:10:00+00:00",
      "date_modified": "2026-09-27T00:00:00+00:00",
      "tags": ["bioclipse","opentox","cheminf","myexperiment"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}