{
  "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/2010/06/17/my-opentox-workshop-contribution-lost.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/wpk6t-snh54",
      "url": "https://chem-bla-ics.linkedchemistry.info/2010/06/17/my-opentox-workshop-contribution-lost.html",
      "title": "My OpenTox Workshop contribution: The Lost Slides",
      "content_html": "<p>During the nice presentations at the recent <a href=\"http://www.opentox.org/data/blogentries/public/opentoxworkshoppotsdam2010\">OpenTox Workshop</a>, I noted that\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2010/05/30/my-opentox-workshop-contribution.html\">My OpenTox Workshop contribution: Linking explicit and implicit knowledge <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\nwas lacking two slides. The slides should have had screenshot of the excellent <a href=\"http://www.bioclipse.net/\">Bioclipse</a> applications\n<a href=\"http://se.linkedin.com/in/olaspjuth\">Ola Spjuth</a> has written in the area of computational toxicology. But here they are.</p>\n\n<h2 id=\"metabolic-fate\">Metabolic Fate</h2>\n\n<p>The metabolic fate of molecules can be predicted with the <a href=\"http://wiki.bioclipse.net/index.php?title=MetaPrint2D\">MetaPrint2D</a> feature (see also the\n<a href=\"http://www-metaprint2d.ch.cam.ac.uk/metaprint2d/\">main MetaPrint2D page</a>). The feature currently uses one specific method, but the immediate feedback\nyou get while drawing molecules, can basically use any model. The currently used model is developed in a collaboration of Ola with Sam Adams (whom we\nall know for his <a href=\"http://jni-inchi.sourceforge.net/\">JNI-InChI</a> library) at Cambridge University and Lars Carlsson at Astra-Zeneca.</p>\n\n<p><img src=\"/assets/images/metaprint2d.png\" alt=\"\" /></p>\n\n<p>This screenshots shows the visual feedback in the (new) <a href=\"http://chem-bla-ics.blogspot.com/search?q=cdk-jchempaint\">JChemPaint</a> editor in Bioclipse, and\non the right we see one interesting Bioclipse feature in action: the <a href=\"http://www.ibm.com/developerworks/opensource/library/os-ecl-cheatsheets/\">cheat sheets</a>.\nThese cheat sheets are inline help documentation which guides the reader through the functionality. But, unlike mere help, cheat sheets can be very\ninteractive and perform some tasks itself, making it easier for the reader to see what was supposed to happen.</p>\n\n<p><em>L. Carlsson, O. Spjuth, S.E. Adams, R.C. Glen, S. Boyer, Use of Historic Metabolic Biotransformation Data as a Means of Anticipating Metabolic Sites\nUsing MetaPrint2D and Bioclipse, accepted in BMC Bioinformatics.</em></p>\n\n<h2 id=\"structural-alerts-etc\">Structural Alerts, etc</h2>\n\n<p>Structural alerts are one method to signal the scientist that the molecule under study needs some more attention (see for example\ndoi:<a href=\"https://doi.org/10.1016/j.mrrev.2008.05.003\">10.1016/j.mrrev.2008.05.003</a>). It helps him decide to continue to look at that particular\nstructure, or to move on. Ola also developed a decision support plugin.</p>\n\n<p><img src=\"/assets/images/ds.png\" alt=\"\" /></p>\n\n<p>One of the cool features is that, in good Bioclipse habits, deliver a pluggable architecture. This practically means, that anyone can add their own\ndecision rules; those can be added as local software, or as services on a central, institute specific server. The results in this screenshot show\nthat a Bursi AMES data-based model estimates that this molecule is mutagenetic.</p>\n\n<p><em>O. Spjuth, L. Carlsson, M. Eklund, E.A. Helgee, S. Boyer, Integrated decision support for assessing chemical liabilities, In preparation</em></p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">BENIGNI, R., &#38; BOSSA, C. (2008). Structure alerts for carcinogenicity, and the Salmonella assay system: A novel insight through the chemical relational databases technology. <i>Mutation Research/Reviews in Mutation Research</i>, <i>659</i>(3), 248–261. https://doi.org/10.1016/j.mrrev.2008.05.003 <a href=\"https://doi.org/10.1016/j.mrrev.2008.05.003\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1016/j.mrrev.2008.05.003\">Scholia</a></div>\n  </div>",
      "summary": "During the nice presentations at the recent OpenTox Workshop, I noted that My OpenTox Workshop contribution: Linking explicit and implicit knowledge was lacking two slides. The slides should have had screenshot of the excellent Bioclipse applications Ola Spjuth has written in the area of computational toxicology. But here they are.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/metaprint2d.png",
      "date_published": "2010-06-17T00:00:00+00:00",
      "date_modified": "2026-09-27T00:00:00+00:00",
      "tags": ["opentox","bioclipse"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1016/j.mrrev.2008.05.003", "doi": "10.1016/j.mrrev.2008.05.003"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}