{
  "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/2009/12/19/december-wrap-up-x-mas-holidays-at-last.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/pxwbm-2wn02",
      "url": "https://chem-bla-ics.linkedchemistry.info/2009/12/19/december-wrap-up-x-mas-holidays-at-last.html",
      "title": "December wrap up. X-mas holidays at last!",
      "content_html": "<p>Wow, I just saw it has been <strong>17 days</strong> since my last post already :( That’s a new record, I think! A lot has happened\nactually, but I have not had time to write up things. Actually, I have still have\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2009/11/25/swat4ls-wrapping-up-1.html\">SWAT4LS coverage left to do <i class=\"fa-solid fa-recycle fa-xs\"></i></a> :(</p>\n\n<h3 id=\"latex\">Latex</h3>\n\n<p>Anyway, one of the things our group has been up to in the last two weeks, is writing a book to support of the\n<a href=\"http://www.pharmbio.org/\">free, online Pharmaceutical Bioinformatics course</a>. The material includes a good deal of\ncheminformatics (molecular representation: chemical graph theory, 3D geometries, file formats, line notations, InChI),\nbioinformatics (sequence analysis), and statistics (PLS, PCA, proteochemometrics). All in light of drug discovery.\nOf course, we’re using LaTeX, and I asked around here and there about related things. For example, on\n<a href=\"http://stackoverflow.com/questions/1901213/open-source-latex-environment-for-educational-books\">StackOverflow on educational book styles</a>.\nBut also on <a href=\"http://friendfeed.com/the-life-scientists/5fd17e31/who-can-point-me-to-drug-where-tautomerism-is\">FriendFeed on tautomerism in relation to drug activity</a>.</p>\n\n<h3 id=\"bioclipse\">Bioclipse</h3>\n\n<p>I also hacked up a <a href=\"http://www.bioclipse.net/\">Bioclipse</a> plugin that allows me to convert a Bioclipse matrix\nresource into LaTeX source code, but that will not be part of the Bioclipse 2.2 release, as it requires quite\nsome updating of the statistics functionality. BTW, the LaTeX plugin is hosted at <a href=\"http://gitorious.org/~egonw\">Gitorious</a>,\nwhich is an GitHub alternative, but <a href=\"http://stackoverflow.com/questions/1913726/has-gitorious-hooks-for-cia-commit-notification\">does not seem to have post-commit hooks</a>\n:(</p>\n\n<p>Also, the Bioclipse2 paper “Bioclipse 2: A scriptable integration platform for the life sciences” has been\npublished now in BMC Bioinformatics (DOI:<a href=\"https://doi.org/10.1186/1471-2105-10-397\">10.1186/1471-2105-10-397</a>)!</p>\n\n<h3 id=\"new-student\">New student</h3>\n\n<p>I am also happy to have a second student starting in January, who will work primarily on an RDF version of the\n<a href=\"http://chembl.blogspot.com/\">ChEMBL</a> data. Her work will extend on the excellent work being done right now by\n<a href=\"http://saml.rilspace.com/\">Samuel on comparing Prolog with DL reasoning</a>.</p>\n\n<h3 id=\"cdk-licensing\">CDK Licensing</h3>\n\n<p>Another thing that required my attention was the problem brought up by Andew on licensing. There was considerable\nout-of-date problems with the statements the <a href=\"http://cdk.sf.net/\">CDK</a> makes on the license and copyright informations\ncertain CDK modules use, and the implications that has on what the CDK project is required to do (e.g. link to source\ncode of third party libraries) and for downstream CDK distributors, like the <a href=\"https://packages.debian.org/libcdk-java\">Debian</a>\nand <a href=\"https://packages.ubuntu.com/libcdk-java\">Ubuntu</a> projects. For example, it\nbecame apparent that the Debian package cannot distribute the XML Schema of <a href=\"http://en.wikipedia.org/wiki/Chemical_Markup_Language\">CML</a>,\nwhich is <a href=\"http://creativecommons.org/licenses/by-nd/2.5/\">CC-BY-ND</a> which is not DSFG-compatible. A few bugs\nhave been reported, and work is ongoing to fix the issues.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Spjuth, O., Alvarsson, J., Berg, A., Eklund, M., Kuhn, S., Mäsak, C., Torrance, G., Wagener, J., Willighagen, E. L., Steinbeck, C., &#38; Wikberg, J. E. (2009). Bioclipse 2: A scriptable integration platform for the life sciences. <i>BMC Bioinformatics</i>, <i>10</i>(1). https://doi.org/10.1186/1471-2105-10-397 <a href=\"https://doi.org/10.1186/1471-2105-10-397\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1186/1471-2105-10-397\">Scholia</a></div>\n  </div>",
      "summary": "Wow, I just saw it has been 17 days since my last post already :( That’s a new record, I think! A lot has happened actually, but I have not had time to write up things. Actually, I have still have SWAT4LS coverage left to do :(",
      
      "date_published": "2009-12-19T00:00:00+00:00",
      "date_modified": "2026-05-30T00:00:00+00:00",
      "tags": ["bioclipse","bioinfo","cheminf","latex"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1186/1471-2105-10-397", "doi": "10.1186/1471-2105-10-397"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}