{
  "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/2009/07/07/bioclipse-jchempaint-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/qj1xp-mas31",
      "url": "https://chem-bla-ics.linkedchemistry.info/2009/07/07/bioclipse-jchempaint-2.html",
      "title": "Bioclipse-JChemPaint #2",
      "content_html": "<p>Recently, I blogged about <a href=\"https://chem-bla-ics.linkedchemistry.info/2009/06/18/bioclipse-jchempaint.html\">Bioclipse-JChemPaint <i class=\"fa-solid fa-recycle fa-xs\"></i></a> of the imminent Bioclipse 2.0.0\nrelease, a complete rewrite of the <a href=\"http://www.bioclipse.net/\">Bioclipse</a> application as published in doi:<a href=\"https://doi.org/10.1186/1471-2105-8-59\">10.1186/1471-2105-8-59</a>.\nI also <a href=\"https://chem-bla-ics.linkedchemistry.info/2009/05/21/bioclipse-beta5-really-last-one-now.html\">blogged <i class=\"fa-solid fa-recycle fa-xs\"></i></a> about the feature to\nbrowse large <a href=\"http://en.wikipedia.org/wiki/Chemical_table_file\">MDL SF files</a> (Bioclipse 2.1 will have support one or more CML\nconventions for chemical tables). Ola did some <a href=\"http://bioclipse.blogspot.com/2009/07/working-with-large-sdfiles-in-bioclipse.html\">profiling on processing SD files</a>,\nbut also notes that such may be more suitable for the StructureDB</p>\n\n<p>Browsing a large set of structures with there properties gives a quick overview of the data set. It also makes bugs shallow,\nsuch as the one shown below found when I was browsing the <a href=\"http://www.chemblog.org/\">StarLite</a> database:</p>\n\n<p><img src=\"/assets/images/jcpRoundingError.png\" alt=\"\" /></p>\n\n<p>The MDL molfile for structure 55 is available from the <a href=\"http://pele.farmbio.uu.se/cgi-bin/bugzilla/attachment.cgi?id=78&amp;action=edit\">bug report I filed against Bioclipse</a>.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Spjuth, O., Helmus, T., Willighagen, E. L., Kuhn, S., Eklund, M., Wagener, J., Murray-Rust, P., Steinbeck, C., &#38; Wikberg, J. E. (2007). Bioclipse: an open source workbench for chemo- and bioinformatics. <i>BMC Bioinformatics</i>, <i>8</i>(1). https://doi.org/10.1186/1471-2105-8-59 <a href=\"https://doi.org/10.1186/1471-2105-8-59\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1186/1471-2105-8-59\">Scholia</a></div>\n  </div>",
      "summary": "Recently, I blogged about Bioclipse-JChemPaint of the imminent Bioclipse 2.0.0 release, a complete rewrite of the Bioclipse application as published in doi:10.1186/1471-2105-8-59. I also blogged about the feature to browse large MDL SF files (Bioclipse 2.1 will have support one or more CML conventions for chemical tables). Ola did some profiling on processing SD files, but also notes that such may be more suitable for the StructureDB",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/jcpRoundingError.png",
      "date_published": "2009-07-07T00:10:00+00:00",
      "date_modified": "2026-09-27T00:00:00+00:00",
      "tags": ["bioclipse","jchempaint","cdk","chembl"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1186/1471-2105-8-59", "doi": "10.1186/1471-2105-8-59"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}