Literate Programming by Donald Knuth (1983) is a seminal book that introduces the concept of literate programming. Using technology available in 2014 we can make a small but important change to the last sentence: This blog post is an example for such a document.

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. The post is about the importance of publication of data and software where currently the rewards are stacked disproportionately in favor of text publications.

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.

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. Scholars will always use Microsoft Word Microsoft Word is of course what almost all authors use in the life sciences and many other disciplines. One big reason for this is the file formats accepted my manuscript submission systems.

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.

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.

Article-level metrics (ALMs) provide a wide range of metrics about the uptake of an individual journal article by the scientific community after publication. They include citations, usage statistics, discussions in online comments and social media, social bookmarking, and recommendations.

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 http://book.openingscience.org.

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. Authoring involves several steps, and it helps to think about them separately: * Writing. Manuscript writing, including formatting, collaborative authoring * Submission.

Last Friday and Saturday the 6th SpotOn London conference tool place at the British Library. I had a great time with many interesting sessions and good conversations both in and between sessions. But I might be biased, since I helped organize the event, and in particular did help put the sessions for the Tools strand together.

This Friday and Saturday the SpotOn London Conference will take place at the British Library in London. I am very excited, as I have come to this conference since the first one in 2008, and have helped organize the event since 2009. The conference is about science communication in the broadest sense, and has three strands that focus on science communication, science policy and tools.