Build Roads not Stagecoaches 18 Jul 2014

I attended the Open Knowledge Festival this week and I had a blast. For three days (I also attended the fringe event csv,conf on Tuesday) I listed to wonderful presentations and was involved in great discussions - both within sessions, but more importantly all the informal discussions between and after sessions.

Literate Blogging 04 Apr 2014

Literate programming is a methodology that combines a programming language with a documentation language, thereby making programs more robust, more portable, more easily maintained, and arguably more fun to write than programs that are written only in a high-level language. The main idea is to treat a program as a piece of literature, addressed to human beings rather than to a computer. The program is also viewed as a hypertext document, rather like the World Wide Web.

Continuous Publishing 10 Mar 2014

Earlier this week Björn Brembs wrote in a blog post (What Is The Difference Between Text, Data And Code?): To sum it up: our intellectual output today manifests itself in code, data and text.

Are static Websites the Future or the Past? 05 Mar 2014

Last week I had a little discussion on Twitter about a great blog post by Zach Holman: Only 90s Web Developers Remember This. The post is not only fun to read, but also reminded me that it is now almost 20 years (1995) that I built my first website - of course using some of the techniques (the one pixel gif!, the   tag!) described in the post.

Six Misunderstandings about Scholarly Markdown 03 Mar 2014

In this post I want to talk about some of the misunderstandings I frequently encounter when discussing markdown as a format for authoring scholarly documents.

From Markdown to JATS XML in one Step 12 Dec 2013

The Journal Article Tag Suite (JATS) is a NISO standard that defines a set of XML elements and attributes for tagging journal articles. JATS is not only used for fulltext content at PubMed Central (and JATS has evolved from the NLM Archiving and Interchange Tag Suite originally developed for PubMed Central), but is also increasinly used by publishers.

What Can Article Level Metrics Do for You? 11 Dec 2013

The scientific impact of a particular piece of research is reflected in how this work is taken up by the scientific community. The first systematic approach that was used to assess impact, based on the technology available at the time, was to track citations and aggregate them by journal. This strategy is not only no longer necessary — since now we can easily track citations for individual articles — but also, and more importantly, journal-based metrics are now considered a poor performance measure for individual articles.

Example article with embedded code and data 11 Dec 2013

In October I published an essay on Article-Level Metrics (ALM) in PLOS Biology (Fenner, 2013). The essay is a good introduction into Article-Level Metrics, and I am proud that it is part of the Tenth Anniversary PLOS Biology Collection. Like all PLOS content, the article was published with a Creative Commons attribution license, allowing me to republish the article on this blog. I have now done so and the article is available here.

Opening Science - the Book 05 Dec 2013

Opening Science: The Evolving Guide on How the Internet is Changing Research, Collaboration and Scholarly Publishing is a SpringerOpen book (using a Creative Commons Attribution-NonCommercial license) that will be published in a few weeks. If you can’t wait for the book to be published and/or you want to make comments or suggestions, go to the dynamic book online version at

The Grammar of Scholarly Communication 17 Nov 2013

Authoring of scholarly articles is a recurring theme in this blog since it started in 2008. Authoring is still in desperate need for improvement, and nobody has convincingly figured out how to solve this problem.

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