{
  "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/2007/07/16/open-science-notebook-10-years-ago.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/m9z3j-c9093",
      "url": "https://chem-bla-ics.linkedchemistry.info/2007/07/16/open-science-notebook-10-years-ago.html",
      "title": "The Open Science Notebook 10 years ago",
      "content_html": "<p>So, with <a href=\"http://mndoci.com/blog/2007/07/14/does-the-open-research-world-need-a-single-access-point/\">all</a>\n<a href=\"http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html\">these</a>\n<a href=\"http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html\">people</a>\n<a href=\"https://doi.org/10.59350/sk1yv-zxp51\">blogging <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\n<a href=\"http://www.sennoma.net/main/archives/2007/07/giving_open_notebook_science_a.php\">about</a>\n<a href=\"http://scilib.typepad.com/science_library_pad/2007/06/thinking-about-.html\">the</a>\n<a href=\"https://blogs.ch.cam.ac.uk/pmr/2007/06/08/alicias-open-science-thesis/\">Open <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\n<a href=\"http://lccccollegeenglish.blogspot.com/2007/05/gary-hermans-open-notebook-science.html\">Science</a>\n<a href=\"https://doi.org/10.63485/c9h8f-ee251\">Notebook <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\n(yes, each word is one distinct blog) it is worth looking back in time. To make clear what I put\nunder the OSN: a notebook in which experimental details and outcome are written down.\nSo, what did the OSN look like almost ten years ago?</p>\n\n<p>It looked like the early open source chemoinformatics projects, such as\n<a href=\"http://sourceforge.net/users/steinbeck/\">CompChem and JMDraw</a> set up by\n<a href=\"http://wiki.cubic.uni-koeln.de/blog/\">Christoph</a> (the SourceForge projects have, unfortunately,\nbeen deleted; so I cannot link to the original project pages). JChemPaint and Jmol also originate from\nthose years.</p>\n\n<p>These projects were OSNs <em>avant le lettre</em>: an experiment in chemoinformatics is the definition of a\nnew (or reformulation of an old) algorithm, writing down the experiment (source code in this code),\nuploaded into a repository (Open Science!) for everyone to comment on, possible sent around an\nannouncement for discussion to mailing list, and reporting the outcome (preferable in a peer-reviewed\njournal). While I am ranting^Wtalking about the issues, chemoinformatics is in the luxurious situation\nthat reproducibility of a procedure is <strong>much</strong> easier,\n<a href=\"https://blogs.ch.cam.ac.uk/pmr/2007/07/14/more-potential-reproducibility/\">except for the missing data part <i class=\"fa-solid fa-recycle fa-xs\"></i></a>.</p>\n\n<p>Just wanted to say that OSN is really nothing new, not to chemistry anyway. Maybe for lab chemists.\n<a href=\"http://drexel-coas-talks-mp3-podcast.blogspot.com/\">Jean-Claude</a> has shown to be very successful in\n<a href=\"https://doi.org/10.1038/npre.2007.39.1\">promoting these open science ideas</a> among lab chemists,\nand congratulate him with the exposure in all those magazine interviews lately. Cheers!</p>\n\n<h2 id=\"open-science-versus-open-source\">Open Science versus Open Source</h2>\n\n<p>Oh, and let me make the distinction between open source in general and open science. Many of the\ncurrent open source software in chemistry(/chemoinformatics) are <strong>not</strong> open science. Open science\nmeans that every step in the development process is open, where is many chemoinformatics programs\nare <em>dumped</em> into the open source sphere at the end. That is not the way it should be.</p>\n\n<p>For the lab chemists: <em><a href=\"http://en.wikipedia.org/wiki/%5EW\">^W is a shortcut for ‘delete the previous word’</a></em>.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Apodaca, R. (2007). Open Notebook Science Using InChIMatic. In <i>Front Matter</i>. Front Matter. https://doi.org/10.59350/sk1yv-zxp51 <a href=\"https://doi.org/10.59350/sk1yv-zxp51\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.59350/sk1yv-zxp51\">Scholia</a></div>\n    <div class=\"csl-entry\">Bradley, J.-C. (2007). Open Notebook Science Using Blogs and Wikis. <i>Nature Precedings</i>. https://doi.org/10.1038/npre.2007.39.1 <a href=\"https://doi.org/10.1038/npre.2007.39.1\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1038/npre.2007.39.1\">Scholia</a></div>\n    <div class=\"csl-entry\">Suber, P. (2007). Blogging open science. In <i>Front Matter</i>. Front Matter. https://doi.org/10.63485/c9h8f-ee251 <a href=\"https://doi.org/10.63485/c9h8f-ee251\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.63485/c9h8f-ee251\">Scholia</a></div>\n  </div>",
      "summary": "So, with all these people blogging about the Open Science Notebook (yes, each word is one distinct blog) it is worth looking back in time. To make clear what I put under the OSN: a notebook in which experimental details and outcome are written down. So, what did the OSN look like almost ten years ago?",
      
      "date_published": "2007-07-16T00:00:00+00:00",
      "date_modified": "2025-07-30T00:00:00+00:00",
      "tags": ["cdk","openscience"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1038/npre.2007.39.1", "doi": "10.1038/npre.2007.39.1"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.59350/sk1yv-zxp51", "doi": "10.59350/sk1yv-zxp51"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.63485/c9h8f-ee251", "doi": "10.63485/c9h8f-ee251"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}