WordPress for Scientific Publishing

This entry is part 1 of 3 in the series Using WordPress

The democratization of publishing is well underway thanks to the internet and tools like WordPress and the MediaWiki software that powers Wikipedia. Sadly, scientific publishing is still living in a feudal age where personal advancement requires publication in “peer reviewed” journals that are too often under the control of for-profit publishing houses.

Erecting a paywall for access to knowledge that was gathered at great public expense seems wrong on many levels.  This post will explore ways to harness WordPress that fit the needs of scientific publishing.

Why WordPress?

One of the things we know to be true about science is that it is hard work.  (If it were easy, everyone would do it.) Many aspects of the scientific process involve working with custom hardware and software, often with little long term support. While there are many scientists and scholars who are also techno-geeks, enamored of modern web tools; there are many more who do not have the extra band-width to master an ever-changing set of web tools. They are already too busy mastering experimental design, data collection, data management, statistics and data visualization — to say nothing of grant writing, publishing, teaching and training, etc.

For these people, WordPress is a very good option as it is mature, free, easy to use and widely supported. Every once in a while it’s nice to use something off-the-shelf as long as it meets our needs.  WordPress is certainly mature and well supported and we suspect that the right suite of plugins can turn it into a powerful tool for scientific publication.

As we slowly master WordPress for scientific publishing, you can help out by suggesting topics that need to be addressed or by calling our attention to plugins or blogs that demonstrate how WordPress can address the needs of scientisits. We will cover those topics in additional posts in this series.

An excellent starting point for upgrading WordPress to be ready for scholarly articles is Joss Winn’s 2009 article on Scholarly publishing with WordPress.

Footnotes

Footnotes have a long history in scholarly publications.  Although their introduction has been attributed to Gibbon, their first use can be traced all the way back to the middle ages. ((Anthony Grafton, The Footnote: A Curious History (Cambridge, MA: Harvard University Press, 1997) )) Footnotes have an important role to play in referencing sources of information without interrupting the flow of a paragraph.  Any serious scholarly writing should make use of footnotes in this capacity as well as to provide a place for textual commentary that would be out of place within the body of an article. ((One example of the use of footnotes for textual commentary would be to elevate astute reader comments to the status of footnotes within the body of the article. This style of footnote allows authors to give credit for valuable input and provide links to additional information while still maintaining control over the readability of an article.))

Among WordPress footnotes plugins the most popular by far is WP-Footnotes. Installation, as with most WordPress plugins, is sinfully easy.  Composing footnotes is just a matter of including the footnote within double parentheses.  The plugin takes care of the rest.

Equations

Anyone that uses math uses equations.  Equations allow us to communicate abstract concepts in a way that is concise and not subject to mis-interpretation. Equations keep us honest. When our audience understands mathematics it is always desirable to include the equations that define precisely what we mean while at the same time providing enough text for the non-mathematical to also understand.

As an example, let’s take a look at exponential decay.  Words can give a basic description:

A quantity experiences exponential decay when it decreases at a rate proportional to its value.

But anyone who has had math beyond calculus may prefer a more explicit explanation:

The equation describing a quantity decreasing at a rate proportional to it’s value is expressed as a differential equation: $\frac{\partial f}{\partial t} = -\lambda t$ .  By integrating with respect to time, we obtain the value of that quantity at any point in time: $f(t) = f_0 e^{-\lambda t}$ . Hence ‘exponential’ decay.

Unfortunately, good looking equations are difficult to construct.  By universal acclaim, the best way to create equations for publication is with the LaTex typesetting system. Those in need of a crash course in composing LaTex typesetting commands may wish to consult Chapter 3 of Tobias Oetiker’s Not So Short Intro to LaTex.

WordPress has several equations plugins, of which all those in active development use LaTex.  The most popular appears to be WP LaTex which we use for this blog.  An excellent example of the use of this plugin is Terry Tao’s equation-filled mathematics blog.

Conclusion

Our experience so far encourages us to recommend WordPress as a tool for writing scientific articles for self-publication, for setting up a small journal dedicated to a specific topic, or simply as an editing tool to prepare articles for submission to an existing journal. Setup is quite easy and enough plugins exist to make for good looking documents.

Over the course of time we will describe additional plugins as we try them out.  Any suggestions would be greatly appreciated.

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