Posts from 2014-07

A first experience with Open Access publishing

Most scientists have found out by now that a lot has been going wrong with scientific publishing over the years. In many fields, scientific journals are no longer fulfilling what used to be their primary role: disseminating and archiving the results of scientific studies. One of the new approaches that were developed to fix the publishing system is Open Access: the principle that published articles should be freely accessible to everyone (under conditions that vary according to which "dialect" of Open Access is used) and that the cost of the publishing procedure should be payed in some other way than subscription fees. The universe of Open Access publishing has become quite complex in itself. For those who want to know more about it, a good starting point is this book, whose electronic form is, of course, Open Access.

While I have been following the developments in Open Access publishing for a few years, I had never published any Open Access article myself. I work at the borderline of theoretical physics and biophysics, which sounds like closely related fields but they nevertheless have very different publishing traditions. In theoretical physics, the most well-known journals are produced by non-commercial publishers, in particular scientific societies. Their prices have not exploded, nor do these publishers put pressure on libraries to subscribe to more than they want to. There is a also a strong tradition of making preprints freely available, e.g. on This combined model continues to work well for theoretical physics, meaning that there is little incentive to look at Open Access publishing models. However, as soon as the "bio" prefix comes into play, the main journals are commercial. Some offer a per-article Open Access option, in exchange for the authors paying a few hundred to a few thousand dollars per article. There are also pure Open Access journals covering this field (e.g. PLOS Computational Biology), whose price range is similar. On the scale of the working budget of a theoretician working in France, these publishing fees are way too high, which is why I never considered Open Access for my "applied" research.

The fact that I have recently published my first Open Access article, in the pure Open Access journal F1000Research, is almost a bit accidental. The topic of the article is the role of computation in science, with a particular emphasis on the necessity to keep scientific models distinct from software tools. I had the plan to write such an artile for a while, but it didn't really fit into any of the journals I knew. The subject is computational science, but more its philosophical foundations than the technicalities that journals on computational science specialize in. The audience is scientists applying computations, which is a much larger group than the methodology specialists who subscribe to and read computational science journals. Even if some computational science journal might have accepted my article, it wouldn't have reached most of its intended audience. A journal on the philosphy of science would have been worse, as almost no practitioner of computational science looks at this literature. Since there was no clear venue where the intended audience would have a chance of finding my article, the best option was some Open Access journal where at least the article would be accessible to everyone. Publicity through social networks could then help potentially interested readers discover it. Two obstacles remained: finding an Open Access journal with a suitable subject domain, and getting around the money problem.

At the January 2014 Community Call of the Mozilla Science Lab, I learned that F1000Research was starting a new section on "science communication", and was waiving article processing charges for that section in 2014. This was confirmed shortly thereafter on the journal's blog. Science communication was in fact a very good label for what I wanted to write about. And F1000Research looked like an interesting journal to test because its attitude to openness goes beyond Open Access: the review process is open as well, meaning that reviews are published with the reviewers' names, and get their own DOI for reference. So there was my opportunity.

For those new to the Open Access world, I will give a quick overview of the submission and publishing process. Everything is handled online, through the journal's Web site and by e-mail. Since I very much prefer writing LaTeX to using Word, I chose the option of submitting through the writeLaTeX service. The idea of writeLaTeX is that you edit your article using their Web tools, but nothing stops you from downloading the template provided by F1000Research, writing locally, and uploading the final text in the end. I thus wrote my article using my preferred tool (Emacs) and on my laptop even when I didn't have a network connection. Once you submit your article, it is revised by the editorial staff (concerning language, style, and layout, they don't touch the contents). Once you approve the revision, the article is published almost instantaneously on the journal Web site. You are then asked to suggest reviewers, and the journal asks some of them (I don't know how they make their choice) to review the article. Reviews are published as they come in, and you get an e-mail alert. In addition to providing detailed comments, reviewers judge the article as "approved", "approved with reservations" or "not approved". As soon as two reviewers "approve", the article status changes to "indexed", meaning that it gets a DOI and it is listed in databases such as PubMed or Scopus. Authors can reply to reviewers (again in public), and they are encouraged to revise their article based on the reviewers' suggestions. All versions of an article remain accesible indefinitely on the journal's Web site, so the history of the article remains accessible forever.

Overall I would judge my experience with F1000Research as very positive. The editorial staff replies rapidly and gets problems solved (in my case, technical problems with the Web site). Open review is much more reasonable than the traditional secret peer review process. No more guessing who the reviewers are in order to please them with citations with the hope of getting your revision accepted rapidly. No more lengthy letters to the editor trying to explain diplomatically that the reviewer is incompetent. With open reviewing, authors and reviewers act as equals, as it should always have been.

The only criticism I have concerns a technical point that I hope will be improved in the future. Even if you submit your original article through writeLaTeX, you have to prepapre revisions using Microsoft Word: you download a Word file for the initially published version, activate "track changes" mode, make your changes, and send the file back. For someone who doesn't have Microsoft Word, or is not familiar with its operation, this is an enormous barrier. A journal that encourages authors to revise their articles should also allow them to do so using tools that they have and are familiar with.

Will I publish in F1000Research again? I don't expect to do so in the near future. With the exception of the science communication section, F1000Research is heavily oriented towards the life sciences, so most of my research doesn't fit in. And then there is the money problem. Without the waiver mentioned above, I'd have had to pay 500 USD for my manuscript classified as an "opinion article". Regular research articles are twice as much. Compared to a theoretician's budget, which needs to cover mostly travel, these amounts are important. Moreover, in France's heavily bureaucratized public research, every euro comes with strings attached that define when, where, and on what you are allowed to spend it. Project-specific research grants often do allow to pay publication costs, but research outside of such projects, which is still common in the theoretical sciences, doesn't have any specific budget to turn to. The idea of the Open Access movement is to re-orient the money currently spent on subscriptions towards paying publishing costs directly, but such decisions are made on a political and administrational level very remote from my daily work. Until they happen, it is rather unlikely that I will publish in Open Access mode again.

Tags: computational science, computer-aided research, emacs, mmtk, mobile computing, programming, proteins, python, rants, reproducible research, science, scientific computing, scientific software, social networks, software, source code repositories, sustainable software

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