Open source & access scientific publication workflow

As we prepare to submit our paper on ship noise in orca habitat I have been seeking an optimal way in which to publish our work. As an independent researcher working for a small non-profit, my publication workflow priorities (in order) were: open access, low costs to authors, easy with opensource tools (e.g. not requiring a Word document!), facilitation of long-range collaboration (my co-authors are not co-located), allowance of supporting materials in diverse formats (e.g. audio files of outlier ships), and open peer review (because I am tired of reviewing without getting any response or credit).

While most of my colleagues have historically published in bioacoustic, biological, or environmental journals, most are either closed access or only offer open access after extracting a pretty penny from the author(s) or after a ~5-year waiting period. For example, the Journal of the Acoustical Society of America is closed access (membership costs ~$100/yr) and PLOSone is charges $1350/article.  It’s a work in progress, but I started building a comparison matrix of open access and other journals that might appeal to marine scientists or bioacousticians.

After a lot of searching and reading about projects like Liberating Research (open peer review) and ShareLaTeX, I homed in on the PeerJ as a potential publisher.   Compared to F1000 and eLife, PeerJ has a clearly defined, progressive, and most-affordable revenue model.  They get rave reviews after only a year of operation, and they are used by my alma mater, Stanford University.

Then I discovered they were promoting themselves by offering free publication for submissions during the month of March!  A quick email to PeerJ asking if a paper on ship noise in an endangered species’s habitat was within their scope (“Biological Sciences, Medical Sciences, and Health Sciences”) got a positive response within a day.  (If and when they expand their scope to include all science is an intriguing question, but for now they seem to be keeping it simple and/or avoiding competition with long-standing entities like arxiv…)

So, now the question was how to move from writing the manuscript (in Libre Office with the Zotero plugin) to submission to first in PeerJ pre-prints, and then in the PeerJ journal.  The simplest route was to just continue in Libre Office and export the paper as a PDF file.  Given PeerJ’s new policy on accepting a single PDF for reviewer use, this would work both the pre-print and the first round of a submission to the PeerJ journal.  If the article was accepted, individual files for each figure and table would need to be provided.

The only problems with this R & GMT figures & tables -> LibreOffice+ZoteroPlugin -> PDF -> PeerJs workflow were that: (1) collaborative writing on the final draft was not going to be as easy as working in something like a Google document that handles simultaneous editing; and (2) the PDF generated by LibreOffice wasn’t going to look as elegant as a PDF generated from a LaTeX editor.  (I’m still spoiled by how great my dissertation looked — thanks to Eric Anderson for the LaTeX inspiration back then!)

This longing for on-line collaboration with remote colleagues and for not having to adjust figure size and table dimensions in LibreOffice anymore sent me towards ShareLatex until I noticed that PeerJ was promoting WriteLaTeX!  Most importantly, WriteLaTeX was offering a PeerJ template and “single-click” submission from WriteLatex to PeerJ pre-prints and/or the PeerJ journal.  Full functionality at WriteLatex will cost ~$39/year, but I think it may be worth it to have all the requisite files transferred over to PeerJ automagically…

So now the most promising workflow looks like: R & GMT figures & tables -> WriteLaTeX + .bib file from Zotero -> PDF -> PeerJs.  Unfortunately, I’m getting bogged down in how to export in bibtex or bibLatex with the citekeys that I know and love, but it looks like there is light at the end of the tunnel…

2 thoughts on “Open source & access scientific publication workflow

  1. Profile photo of Alberto PepeAlberto Pepe

    Hi Scott- I also wanted to point out Authorea for collaborative (LaTeX and non-LaTeX) authoring workflow. Bonus 1: it’s built around the notion of open science. Bonus 2: it integrates natively with scientific notebooks, such as IPython and d3.js (e.g. R integration is possible via the Rmagics IPython package but full R integration is coming soon.

    1. Profile photo of Scott VeirsScott Veirs Post author

      Thanks, Albert. I hadn’t heard of Authorea, but have gotten an account and will try it out. At first glance, I like being able to check out sections while collaborating with co-authors.

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