{
  "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/2008/02/05/performance-c-c-c-java-perl-and-python.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/kktab-e6159",
      "url": "https://chem-bla-ics.linkedchemistry.info/2008/02/05/performance-c-c-c-java-perl-and-python.html",
      "title": "Performance: C, C++, C#, Java, Perl and Python",
      "content_html": "<p>Mathieu Fourment (et al.) just published a paper on some performance testing on 6 programming languages in\n<a href=\"http://www.biomedcentral.com/bmcbioinformatics\">BMC Bioinformatics</a>: <em>A comparison of common programming languages used\nin bioinformatics</em> (doi:<a href=\"https://doi.org/10.1186/1471-2105-9-82\">10.1186/1471-2105-9-82</a>). The below figure is from\nthe paper, for a sequence alignment exercise (copyright with paper authors, OpenAccess license of journal):</p>\n\n<p><img src=\"/assets/images/alignment.gif\" alt=\"\" /></p>\n\n<p>Nothing shocking, I’d say; Java is similar in performance to C++.</p>\n\n<p>What I’d love to have seen, was the performance of compiled Java too, using the java compiler (<em>gcj</em>) which comes with\nGCC 4.1.1. No idea why that was left out. One could also question why they did not use the 1.6 JVM of Sun,\nwhich is more faster (see <a href=\"https://chem-bla-ics.linkedchemistry.info/2006/08/01/cdk-and-java-6-beta.html\">these results on running the CDK unit tests <i class=\"fa-solid fa-recycle fa-xs\"></i></a>).\nAnd, a major omission is Fortran.</p>\n\n<p>Anyway, the authors provide <a href=\"http://www.bioinformatics.org/benchmark/\">the source code</a>, so we can easily test\nourselves the effects of that.</p>\n\n<p>BTW, first post? :) <strong>update:</strong> At least I beat <a href=\"http://cszamudio.spaces.live.com/blog/cns!9BCF6F9D6772B8F5!1742.entry\">Carlos</a>.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Fourment, M., &#38; Gillings, M. R. (2008). A comparison of common programming languages used in bioinformatics. <i>BMC Bioinformatics</i>, <i>9</i>(1). https://doi.org/10.1186/1471-2105-9-82 <a href=\"https://doi.org/10.1186/1471-2105-9-82\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1186/1471-2105-9-82\">Scholia</a></div>\n  </div>",
      "summary": "Mathieu Fourment (et al.) just published a paper on some performance testing on 6 programming languages in BMC Bioinformatics: A comparison of common programming languages used in bioinformatics (doi:10.1186/1471-2105-9-82). The below figure is from the paper, for a sequence alignment exercise (copyright with paper authors, OpenAccess license of journal):",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/alignment.gif",
      "date_published": "2008-02-05T00:00:00+00:00",
      "date_modified": "2025-07-30T00:00:00+00:00",
      "tags": ["java"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1186/1471-2105-9-82", "doi": "10.1186/1471-2105-9-82"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}