A keynote is a presentation typically given at a start of a conference that sets the central theme for the event. A keynote speaker usually has more time (45-60 min) than other presenters, and has the full attention of everyone attending the conference.

Figures are an important part of any scientific document. While the kind of figure commonly used obviously varies between disciplines, charts are an important part of many publications.

Altmetrics track the impact of scholarly works in the social web. Article-Level Metrics focuses on articles, but also looks at traditional citations and usage statistics. The PLOS Article-Level Metrics project was started in 2008. The altmetrics manifesto was published in October 2010 and described the fundamental ideas. By October 2011 we had a number of altmetrics tools, fueled by the Mendeley/PLOS API programming contest.

A few weeks ago Kafkas et al. (2013) published a paper looking at current patterns of how datasets o biological databases are cited in research articles, based on an analysis of the full text Open Access articles available from Europe PMC.

Scholarly documents often need metadata that describe them: typically author(s), title and location (DOI or URL), but possibly many other things. For some metadata it makes sense to store them in the document text, e.g. as is typically done for citations. The problem is that this can make it hard to make the metadata machine-readable.

This paper in markdown format was written by Ethan White et al. The markdown file and the associated bibliogaphy and figure files are available from the Github repository of the paper. I used this version, an earlier version was published as PeerJ Preprint. Special thanks to Ethan White for allowing me to reuse this paper.

After the post last week and the crazy discussion that followed I would understand that you feel you have heard enough about citations in markdown. But I had the feeling last week that something was still missing, and I have done some more thinking.

One important outcome of the recent Markdown for Science workshop was an overall agreement that all the different implementations (or flavors) of markdown that currently exist are a big problem for the adoption of Scholarly Markdown and that we need: As described by Karthik Ram (31 flavors is great for ice cream but not markdown), me and others, there is really a large number of markdown implementations to choose from, includingJohn Gruber’s

In the comments on Monday’s blog post about the Markdown for Science workshop, Carl Boettiger had some good arguments against the proposal for how to do citations that we came up with during the workshop. As this is a complex topic, I decided to write this blog post. Citations of the scholarly literature are an essential part of scholarly texts and therefore have to be supported by scholarly markdown.

One of the important discussions taking place at the Markdown for Science workshop last weekend was about the definition of Scholarly Markdown.

This is the last Gobbledygook post on PLOS Blogs, and at the same time the first post at the new Github blog location. I have been blogging at PLOS Blogs since the PLOS Blogs Network was launched in September 2010, so this step wasn’t easy. But I have two good reasons. In May 2012 I started to work as technical lead for the PLOS Article-Level Metrics project.