{
  "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/2008/07/22/peer-reviewed-chemoinformatics-why.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/10.59350/7z23e-kmf12",
      "url": "https://chem-bla-ics.linkedchemistry.info/2008/07/22/peer-reviewed-chemoinformatics-why.html",
      "title": "Peer reviewed Chemoinformatics: Why OpenSource Chemoinformatics should be the default",
      "content_html": "<p>The battle for scientific publishing is continuing: openaccess, peer reviewing, how much does it cost, who should\npay it, is the data in papers copyrighted, etc, etc.</p>\n\n<p>The battle for chemoinformatics, however, has not even started yet. The Blue Obelisk paper\n(doi:<a href=\"https://doi.org/10.1021/ci050400b\">10.1021/ci050400b</a>) has gotten a lot of attention, and citations. But\nclosed source chemoinformatics is doing fine, and have not really openly taken a standpoint against open source\nchemoinformatics. Actually, <a href=\"http://www.cambridgesoft.com/\">CambridgeSoft</a> just\n<a href=\"http://www.biospace.com/news_story.aspx?StoryID=103955&amp;full=1\">received a good investment</a>. I wonder how this\ninvestment will be used, and where the ROI will come from. More closed data and closed algorithms? Focus on\nservices? Early access privileges? At least they had something convincing.</p>\n\n<p>There are many degrees of openness, and many business models. I value open source chemoinformatics, or chemblaics,\nas I call it. There is a striking similarity between publishing and chemoinformatics. Both play an important role\nin the progress of sciences. A big difference is that (independent) peer review of published results is done in\nscientific publishing, but not generally to chemoinformatics. Surely, algorithms are published… Ah, no; they are\nnot. They are described. Ask any chemoinformatician why this subtle difference is causing headaches…</p>\n\n<p>Let me just briefly stress the difference between core chemoinformatics, and GUI applications. The first <em>must</em>\nbe opensource, to allow <strong>independent</strong> <em>Peer Review</em>; the latter is just nice to have as opensource.\n<a href=\"http://www.bioclipse.net/\">Bioclipse</a> is the GUI (doi:<a href=\"https://doi.org/10.1186/1471-2105-8-59\">10.1186/1471-2105-8-59</a>),\nwhile the <a href=\"http://cdk.sf.net/\">CDK</a> is our peer-reviewed chemoinformatics library\n(pmid:<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/16796559\">16796559</a>). I would also like to stress that the CDK is\n<a href=\"http://www.gnu.org/licenses/lgpl.html\">LGPL</a>, allowing the opensource chemoinformatics library to be used in\nproprietary GUI software. We deliberately choose this license, to allow embedding in proprietary code. The\n<a href=\"http://icodons.com/iCODONS/introducing-java-molecular-descriptor-library/\">Java Molecular Descriptor Library</a>\nof <a href=\"http://icodons.com/\">iCODONS</a> is an example of this (that is, AFAIK it’s not opensource).</p>\n\n<p>So, getting back to that CambridgeSoft investment. I really hope they search the ROI in the added value of the\nuser friendly GUI, and not in the chemoinformatics algorithm implementations, which, IMHO, should be peer-reviewed,\nthus open source. Meanwhile, I will continue working on the CDK project to provide open source chemoinformatics\nalgorithms implementations, for use in opensource <em>and</em> proprietary chemoinformatics GUIs.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Guha, R., Howard, M. T., Hutchison, G. R., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J., &#38; Willighagen, E. L. (2006). The Blue Obelisk—Interoperability in Chemical Informatics. <i>Journal of Chemical Information and Modeling</i>, <i>46</i>(3), 991–998. https://doi.org/10.1021/ci050400b <a href=\"https://doi.org/10.1021/CI050400B\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1021/CI050400B\">Scholia</a></div>\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 class=\"csl-entry\">Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., &#38; Willighagen, E. (2006). Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics. <i>Current Pharmaceutical Design</i>, <i>12</i>(17), 2111–2120. https://doi.org/10.2174/138161206777585274 <a href=\"https://doi.org/10.2174/138161206777585274\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.2174/138161206777585274\">Scholia</a></div>\n  </div>",
      "summary": "The battle for scientific publishing is continuing: openaccess, peer reviewing, how much does it cost, who should pay it, is the data in papers copyrighted, etc, etc.",
      
      "date_published": "2008-07-22T00:00:00+00:00",
      "date_modified": "2008-07-22T00:00:00+00:00",
      "tags": ["cheminf","blue-obelisk"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1021/CI050400B", "doi": "10.1021/CI050400B"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.1186/1471-2105-8-59", "doi": "10.1186/1471-2105-8-59"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.2174/138161206777585274", "doi": "10.2174/138161206777585274"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}