Collaboration in academic writing: software and beyond

Unfortunately, collaboration in academic writing often causes frustration. Academics are used to think that co-authoring a manuscripts means emailing back and forth Microsoft Word documents with endless “Track Changes” and “Comments” layered on top of each other. Whereas writing is dominated by Microsoft Word, citation is dominated by EndNote. These expensive solutions are probably favored by universities because they inflate budgets and staff of IT Departments by keeping people suitably occupied with resolving bugs and crashes. Whatever it is, one can’t avoid collaborating with colleagues who use different systems, so here is my experience, pointing that it is both software and other factors which determine success of collaboration.

1. After we have decided to prepare a joint paper I ask potential co-authors what software they use. Upon hearing that I use Microsoft Word sparingly because it is not an ideal writing software, my colleagues often roll up their eyes (‘oh, one of  those Mac fanatics!‘) and sometimes raise the issue of ‘compatibility’. Concerns over ‘compatibility’ disguise lack of structured thinking about forms and tools of joint academic writing and thinking. So I explain my own writing workflow (OmniOutliner → Byword → Scrivener → Word, all supported by Papers). If the co-author has never heard of such software I always propose that s/he tries it for the period of our collaboration (there are good trial periods as well as PC versions for most of the apps). I also introduce them to the Dropbox and sometimes Google Drive so that we can easily share files and collaboratively edit texts, if needed. Then we agree on the distribution of roles and the stages of collaboration.

2. At the first stage of writing we always prepare a detailed outline of the future manuscript. I use OmniOutliner for this purpose. OmniOutliner is great for collective thinking if your screen can be projected on the white wall or shared across computers with Skype or WebEx. Seeing how OmniOutliner works often makes my PC-Word colleagues respectfully talk about ‘those Aleh’s outlines’. Of course, outlining can be done in Google Docs, MS Word, Scrivener, Pages or other software and supported by mind-mapping applications (I use MindNote Pro and now increasingly Tinderbox).

3. After the draft outline has been prepared, we start writing. I believe in the three drafts concept and that there are benefits in sharing and discussing all of them. Since I produce the first (‘put-it-down‘) draft in Byword or Scrivener, I need to compile it (sometimes by simple copy-and-pasting) to Word or Google Docs for sharing with colleagues who do not use this software. My most frequent co-authors, however, are all Scrivener converts so we simply share Scrivener files through the Dropbox. Scrivener has Revision and Comment tools which I find fully sufficient for discussing earlier drafts. If such drafts contain citations I simply insert Papers citekeys through their MagicManuscripts. I do not format bibliographies in early drafts.

4. After receiving comments on the first draft I usually come back to Scrivener (even if it requires copying and pasting or importing the text back from Word or Google Docs). This is not unusual: Michelle Muto, a writer and a recent MPU guest has a similar workflow. The reason is that the 2nd (‘fix-it-up‘) draft usually requires re-thinking, re-structuring and re-writing which is much easier in Scrivener.

5. The finishing touches in the 3rd (‘dental‘) draft are usually done in Microsoft Word with its ability to carefully track changes and automate dealing with captions and cross-references as well as tables. Many publishers also need submissions in Microsoft Word. This is also the stage for formatting citations and bibliographies according to publisher’s requirements as well as inserting final figures (often prepared with help of OmniGraffle). I have recently described some issues and solutions of collaborating with authors who use Papers. As of now, there are still concerns with in Microsoft Word not always properly handling Papers citations (see e.g. this post from Mekentosj), but they are solvable.

I have recently collaborated with a colleague who used EndNote on a PC. Some of the citations were inserted by him and some other added by me through Papers. He handled the final journal submission. I marked all references cited in this manuscript with a specific keyword (which I highly recommend in any case so that you can quickly refer to the list of citations in all your past manuscripts). Then I created a Smart Collection based on this keyword, exported all references in the collection as an EndNote XML library and emailed to my colleague. Voila! No glitches.


About Aleh Cherp

Aleh Cherp is a professor at Central European University and Lund University. He researchers energy and environment and coordinates MESPOM, a Masters course operated by six Universities.
This entry was posted in Bibliographies, Collaboration, Writing and tagged , , , , , . Bookmark the permalink.

17 Responses to Collaboration in academic writing: software and beyond

  1. Csaba Pusztai says:

    It is a funny thing that people outside the (natural) sciences need to tinker with a handful of applications to get their academic workflows going. Natural science guys probably just laugh and stick with LaTex for the writing. I also like to fiddle with new apps, but sometimes I realize that too much ‘exploration’ for more productive solutions, kind of ironically, has a negative effect on ever realizing those performance gains (‘exploitation’). Exploration, at least in my case, is at least partially fueled by the fact that there is no silver bullet. Although, I strongly believe there could be one. Just very recently I picked up Papers again (I was there to use it at the very very beginning when Mekentosj released the first version. But then got into Sente.) The problem with these competing software is that neither is clearly superior to the other. Sente served me well while writing my dissertation. But I was never very happy with the implementation of highlighting (slow, especially on the iPad). Now I am challenged by having to work cross-platform. At work, I have a PC, at home a Mac, and an iPad on the go. Luckily for me, Scrivener now has a Windows version, so I deposit my .scriv documents in Dropbox and edit them from both PC and Mac. Unfortunately, Sente is not available for PC. Hence the interest in Papers again, which now ships for PC, too. (No highlighting in the PC version yet!!!!). I deposit my Papers library in Dropbox as well. Too bad, Mellel does not support Papers, so bibliographies can’t be formatted automatically, which essentially means that the final draft has to be done in Microsoft Word. Too bad.

    Simultaneously with trying to set up a fluid workflow relying on newer and newer versions of apps, I also exercise a great deal of conservatism. I set everything in the Courier New typeface. Probably considered the ugliest font by many, I find it perfect for on-screen work. It is not there as a default font on computers without a reason. I think its monospace quality makes it perfectly legible. I even set a whole slideshow in Courier very recently. And I got complements from people after the presentation for the typesetting. 😉


  2. Aleh Cherp says:

    Csaba, with all due respect to “natural science guys” I don’t see how LaTex would help them to compose an abstract for a conference (Byword), a cover letter for a job application (also Byword), or an outline for a manuscript (OmniOutliner). I am also doubtful that it can fully handle management of pdf articles and citations (as is done in Papers or Sente), preparation of figures (AI or OmniGraffle), or collective editing (Google Docs). May be these guys don’t need all these things but then my workflow is clearly different. I suspect that the truth is you do need to tinker with different applications to develop “an ecosystem” in which your academic work will occur.


    • simlap says:

      Latex is supported by Papers and Sente. I drag and drop a citation from Sente and it inserts the correct Latex code automatically. When I publish the file to PDF, I ask Sente to produce a .bib, and it inserts the citations and a full bibliography.

      Obviously, Byword and an outliner still have uses. In the lifespan of a paper, I may use all 3 apps to write.


  3. Csaba Pusztai says:

    I am not in close touch with that many natural scientists, This is more an impression I have had seeing many of their documents being produced (including complete books) evidently in LateX. I remember fiddling around with LaTex when I first heard about it many years ago. It seemed to offer quite some power and flexibility (at the expense of other qualities, of course). I needed a quick fix back then, and with LaTex I faced a very leveled learning curve. I liked how it could convert in-text citations into hyperlinks to the end-of-the-document references right away. I am not sure if this is implemented in any wordprocessor yet? (Maybe Word, but definitely not Scrivener or Mellel)
    Yep, I don’t question the need for tinkering, my comment was more related to the challenges in finding an “optimal” ecosystem. It is ever evolving system, for sure. The question is how progressive does one want to be, always looking for a potentially superior solution? Often the transition is not smooth and comes more like a “structural break” (e.g., your MailTags experience).


  4. The power of using latex is that everything is stored in plain text. That means that you can simply use version control software (CVS, SVN, Mercurial, Git) for collaborative writing. It’s simple and the results are beautiful. And yes, many of us use TeX for writing abstracts, cover letters, and outlines, not to mention presentations, books, and…well, anything that involves text.


  5. Aleh Cherp says:

    Thanks, David. I guess there is a place for LaTex and once you’ve learned it you may want to use it for various purposes. I think one needs both capacity and motivation to learn LaTex and these two factors together are very rarely present in social scientists (for a simple reason that they don’t need equations). Since they don’t learn LaTex they don’t use it (as it’s barely something you can just start using). That’s why it’s not a widely adopted technology among social scientists. I am struggling with a much more modest challenge of how to wean people from MS Word and PowerPoint on a Mac. I must say even here I am not very successful because a lot of people are just not motivated to be more productive. I wish, nevertheless, someone could show LaTex to me.


    • David Ketcheson says:

      Actually, I don’t think learning laTeX is worthwhile if you don’t need to typeset mathematical formulas. It does many other things very while, but that’s the “killer feature”. Then again, I don’t have enough experience with the alternatives to say.

      In a similar vein, I use Vi for all my text-editing. It’s useful when editing a paper, but the reason I learned it is because I write a lot of computer code, and something like Vi or Emacs is indispensable for that. But I wouldn’t suggest that someone learn Vi if they don’t write computer code.


  6. Thanks for taking your responsibility as a (digital) scholar seriously. Great post to feed my network with.


  7. Pingback: Collaboration in academic writing: software and beyond | Everything Scrivener

  8. Dellu says:

    I use latex to do all my formal writing; abstracts, class-room papers , articles, thesis etc. But, that doesn’t stop me from tinkering with these apps. Latex can do almost everything that the other apps do. But, some of the apps do it in a more elegant way that I couldn’t stop looking for them.
    -Most latex editors can manage writing projects, but none of them can do it as beautifully as Scrivener.
    -They can not outline as elegantly as OmniOuliner or Neo.
    -No software can effectively tag ideas/points, except Ms OneNote, as Ponies Notebook
    -Tinderbox is the best for connecting and comparing ideas (most expensive and hardest to learn…Latex is easier to learn than Tinderbox …and still it can not even import images!). I was really hoping to rely on it, kill all other apps and concentrate on my work. Unfortunately, it is primitive in many ways: exporting, importing, character recognition.
    It is hard to get an app that can do everything effectively. They usually aren’t good in some ways but do great in others. That is why we always struggle with them. I am struggling to have a solid workflow; i don’t want to migrate to a new app in the middle of my study. Migrating from Ms Onenote was a lot of pain for me. I also don’t want to many tools because they can become disturbances by themselves.


  9. Pingback: It’s not Macs vs. PCs. It’s people vs. powerpoints | Academic workflows on Mac

  10. Amaru says:

    I would agree that opening up more options for writing in the academic world is becoming increasingly pressing. My work revolves around: Vim (you can make it do almost anything you can imagine and then some), LaTeX (no othe software produces more beautiful documents), DEVONThink (everything buckets but has its use) and Scrivener.

    – Vim + LaTeX for syllabi, handouts, lesson plans, quizzes, letters (with letterhead) and brochures

    – Vim + Markdown + Pandoc: note taking, outlining and any document that need light but professional formatting

    – DEVONThink + Vim: research notes, dossiers for writing projects

    – Scrivener + Mendeley + LaTeX: dissertation, papers, fiction


  11. Axel Muller says:

    Hi, I just came across your post now. I was wondering what you think off VUE ( as an alternative to Tinderbox.


  12. Pingback: Color-coding scrivenings in Scrivener | Academic workflows on Mac

  13. Ali says:

    Hello there, any chance your view on collaboration softwares has changed in the past few years as things have evolved? I’m looking to set up my workflow for my dissertation and am quickly finding no one-fits-all solution. I was hoping for a decent citation manager which can handle pdfs, notes, highlights etc (I’m considering Pages but have played with Bookends) and a writing program which is solid for both writing as well as supporting easier collaboration – along the vein of google docs’ real time edit (though I don’t thing such a thing yet exists). I often write drafts and send to multiple people for input and want to reduce the amount of work required to re-combine back into one draft when receiving essentially new and separate documents back from each co-author after they supply their suggestions.

    Although I would not use it for dissertation, I have been impressed with how much Google docs has vastly improved recently with formatting etc. In addition it now has a Research Tool which integrates with the web and Google scholar to provide citations and references as well as web and image search of free licence photos. The key strength of course is the simultaneous or real time editing. Any chance you know of tools or have used tools which don’t require sign up of the collaborators? I looked at Authorea but then discovered it needed a sign in…


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