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.

I think it is fair to say that commenting on scientific papers is broken. And with commenting I mean online comments that are publicly available, not informal discussions in journal clubs or at meetings. This definition would include discussions of papers on social media such as Twitter or Facebook. Why do I think that commenting is broken? * the number of papers with online comments is low.

Yesterday PLOS Biology published an essay by me: What Can Article Level Metrics Do for You? (Fenner, 2013). I had help from many others in writing the essay, in particular PLOS Biology editor Emma Ganley. I hope that the essay can help researchers get introduced to article-level metrics, and I am honored that the essay is part of the PLOS Biology 10th anniversary collection.

Open access to research data is becoming increasingly important, as manifested by memos or press releases from the Wellcome Trust, the European Commission, and the the Office of Science and Technology Policy (OSTP) from the White House.