{
  "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/2009/01/16/bioclipse-and-gist-integration.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/gkcs6-62t68",
      "url": "https://chem-bla-ics.linkedchemistry.info/2009/01/16/bioclipse-and-gist-integration.html",
      "title": "Bioclipse and Gist integration",
      "content_html": "<p>As you might have read, <a href=\"http://www.bioclipse.net/\">Bioclipse</a> has scripting support (see for example, <a href=\"https://chem-bla-ics.linkedchemistry.info/2008/11/20/scripting-jchempaint.html\">Scripting JChemPaint <i class=\"fa-solid fa-recycle fa-xs\"></i></a>),\nand that we have been collection them on <a href=\"http://gist.github.com/\">Gist</a> and indexing them on Delicious with the tags <a href=\"http://delicious.com/tag/bioclipse+gist\">bioclipse and gist</a>.\nThis provides a nice overview of what you can do with the current SVN version of Bioclipse2. And, hopefully, when released, allow users to quickly learn about Bioclipse features,\nallow people to share scripts etc. Think of it as <a href=\"http://myexperiment.org/\">MyExperiment.org</a> for Bioclipse.</p>\n\n<p>Now, what was missing until today, was easy access to gists in Bioclipse itself. No <code class=\"language-plaintext highlighter-rouge\">gist.load(33421)</code> yet. There still is not, but I uploaded earlier today a Wizard for it.\n(The manager will follow later). Right click on an open Project, select New -&gt; Other, and pick <em>Download Gist</em>:</p>\n\n<p><img src=\"/assets/images/gist3.png\" alt=\"\" /></p>\n\n<p>and click <em>Next</em>:</p>\n\n<p><img src=\"/assets/images/gist4.png\" alt=\"\" /></p>\n\n<p>Then, just type the number of the Gist you want to open in Bioclipse, for example <a href=\"http://gist.github.com/18315\">18315</a> (see\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2008/10/25/bioclipse2-scripting-1-from-smiles-to.html\">Bioclipse2 Scripting #1: from SMILES to a UFF optimized structure in Jmol <i class=\"fa-solid fa-recycle fa-xs\"></i></a>),\nand click another <em>Next</em> to select a file name and location:</p>\n\n<p><img src=\"/assets/images/gist5.png\" alt=\"\" /></p>\n\n<p>The current code does require you to know the Gist number, so you’ll need a web browser to look it up, but we do have search facilities in mind. Also, while the code\nattempts so, the resulting Gist is not automatically openend in an editor (a bug). Another idea is to just install the\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2008/10/24/git-eclipse-integration.html\">egit <i class=\"fa-solid fa-recycle fa-xs\"></i></a> plugin in Bioclipse :)</p>",
      "summary": "As you might have read, Bioclipse has scripting support (see for example, Scripting JChemPaint ), and that we have been collection them on Gist and indexing them on Delicious with the tags bioclipse and gist. This provides a nice overview of what you can do with the current SVN version of Bioclipse2. And, hopefully, when released, allow users to quickly learn about Bioclipse features, allow people to share scripts etc. Think of it as MyExperiment.org for Bioclipse.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/gist3.png",
      "date_published": "2009-01-16T00:00:00+00:00",
      "date_modified": "2025-10-26T00:00:00+00:00",
      "tags": ["bioclipse","git","github"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}