Authorea: the future of scientific writing?

It’s fair to say that LaTeX has gained widespread acceptance as the tool of choice for writing scientific scholarly articles (if you need convincing, see here, here and here). In comparison to a typical “what you see is what you get” (WYSIWYG) editor like Microsoft Word or Apache OpenOffice, the most radical aspect of LaTeX is that you don’t immediately see how your document will be typeset. Documents are instead prepared by writing a plain text input file that includes markup commands to specify the formatting, before invoking the LaTeX program to (typically) generate a final PDF document.

Since the LaTeX software and associated text editors like Texmaker are free to download, most scientists do all their document preparation on their own computer. While this is a perfectly valid workflow, it fails to take advantage of the fact that we now live in a web-enabled and highly interconnected world. As Alberto Pepe noted in his presentation at the I Annotate 2013 conference in San Fransisco, today’s scientists are doing 21st century science, writing up using 20th century writing tools (e.g. Microsoft Word, LaTeX), then locking that text away in a 17th century format (i.e. the PDF of a journal paper today has much the same format and accessibility as a scanned copy of a journal article from hundreds of years ago).

In an attempt to bring scientific writing into the 21st century, a number of online LaTeX editors have begun to appear in recent years. An obvious advantage to online editing is that you don’t need to have LaTeX installed on your machine, however since installation is both free and relatively straightforward, this hardly represents a compelling reason for scientists to change the way they write. Instead, it’s the opportunity for collaboration and sharing that has the science community so excited about online LaTeX editing.

Online LaTeX editing is an area that many people are trying to innovate in at the moment (I came across a number of “sorry we’re shutting down because we couldn’t make any money” posts in researching this article), however the two editors that have gained the most traction are ShareLaTeX and writeLaTeX. In a nutshell, these editors are to LaTeX what Google Docs is to WYSIWYG editors like Word and OpenOffice. External collaborators can view and edit the document and there are comment and chat features for discussing changes. They also provide a kind of WYSIWYG functionality, as the PDF output can be generated alongside the text editor as you type. While this is an exciting step forward, the end result for a document on ShareLaTeX and writeLaTeX is still a PDF that locks away the text in that familiar 17th century (and not to mention proprietary) format. To fully exploit the advantages of the web, a different model is clearly needed.

Alberto Pepe and his co-founder Nathan Jenkins might just be on the way to establishing that new 21st century model for scientific writing and publishing. At the most basic level, their new website Authorea offers most* of the features that ShareLaTeX and writeLaTeX do in terms of collaborative editing and commenting. In fact, their referencing (just put in a DOI and it figures out the rest), backup (you can link to your GitHub account** instead of just DropBox), PDF / Microsoft Word export (pick a journal and it will format accordingly) and IPython notebook (you can include the code that was used to generate your figures – see here for an example) functionality represents a step forward on their competitors. At a higher level, Authorea provides a way forward from that 17th century publishing format. While it does allow authors to export to PDF (or Word), the most novel thing about Authorea is that it complies your LaTeX text (or Markdown, which may be the future of scholarly writing – see here) to HTML. Instead locking your text away in a proprietary format, Authorea makes it available on the web for anyone to view and comment on.

One of the most exciting advances in scientific publishing in the last few years has been the rise of pre-print servers like arXiv. Since there is such a long time-lapse between when authors submit a manuscript and when the work is finally published, scientists are posting their work (in PDF format) to a pre-print server as soon as it’s done, so that the wider community can read their work while it’s being reviewed. In a recent interview, Nathan revealed that his “crazy long-term dream” is to fundamentally change the way that pre-publishing works. His hope is that people will pre-publish with Authorea instead, whereby their article is available in HTML format and people can comment directly on different sections of the text. This model is essentially a mix between old-school PDF journal articles and new-age blog posts, which is why there’s so much buzz around Authorea at the moment (e.g. see reviews on AppStorm and AppVita).

I recently created an account for my PhD thesis, so why not give Authorea a try for your next journal paper or manuscript?

 
*It should be noted that with writeLaTeX and ShareLaTeX you basically get complete access to all of the markup commands and packages that LaTeX offers. Authorea makes some minor compromises in order to compile to HTML, which are outlined in this handy cheat sheet. In other words, they cater to the needs of the vast majority of LaTeX users, but if you’re in the advanced minority of users who require highly specific figure or output formatting options then writeLaTeX or ShareLaTeX might be a better option.

**ShareLaTeX has also just introduced a way to link with GitHub, however GitHiub is the only option. In principle, you can sync Authorea with any external hosting service that is compatible with git (e.g GitHub, BitBucket, SourceForge, etc)