Teaching basic lab skills
for research computing

Publishing on the Web

Back in December, I asked a question on the Software Carpentry issue track: What should we teach about writing/publishing papers in a webby world? It led to a lively discussion about how the web is changing scientific publishing, the tools people can use to take advantage of those changes, and the gap between what's possible and what publishers (and senior academics) will actually accept. Many commenters dove immediately into the details of specific tools, but Justin Kitzes nailed it when he said:

I think the biggest hurdle, and most important teaching point, is simply the idea of writing papers in plain text (regardless of the markup language)... There are lots of advantages to plain text...but in the context of the bootcamp, one of the biggest is that it provides a really good use case for version control..

The elephant in the room for students, of course, is (a) why they should change to a practice (leaving Word) that will be viewed as strange and potentially difficult by other collaborators, and (b) more specifically, how they will interact with collaborators who only use Word for track changes and commenting. I don't know that I have good answers to either of these questions.

A few comments later, Cameron Neylon chimed in:

I think it could be worth taking a step back and re-phrasing the question a little. Is the object to teach those building tools about publishing in general (i.e., what tools and hacks might be useful to create) or is the focus here specifically on how to get better incorporation of code into published work? I think the latter is the focus but it might be good to be explicit.

On that basis it would be good in my view to touch on some background in literate programming to give people a bit of context and then look at various authoring tools (knitr, IPyNB, Sweave, Dexy...others presumably) alongside various code repositories and data repositories in that light. This would then provide a way of thinking about the available tools as a way of telling the story, which is different to how they are generally used in practice to manage code and records and actually do the work.

It's a personal bias, but I'd also be inclined to spend some time on the sausage making of the publishing process and why it doesn't fit with what the tools above. What gaps are there? How could they be filled? What would the optimal system look like? What formats would be used?

Carl Boettiger then added his recommendations, which I've condensed as:

  • Start with data publishing and code publishing.
  • Endorse plain text for publications.
  • Address the pain points:
    • Journal submission software
    • Collaboration
    • Citations
  • Dynamic documents: more important to teach the concept than the specifics.

He also said later (in a comment on an early draft of this post) that:

...the opening question asked about "publishing in a webby world", while current publishers and practices are inherently non-webby. This creates a tension I think we never quite resolve. We're stuck tackling the question of how to do "webby publishing in a non-webby world"...

At this point I pushed back a bit based on conversations with bootcamp attendees:

Word is easier to use for normal tasks (like writing a paper with bullet points and italics) than Markdown, much less LaTeX—it's only Stockholm Syndrome that makes us believe otherwise :-). And as long as both senior faculty and journals require people to submit Word (or PDFs derived from specific Word templates), it's hard for us to say, "No, really, version control is better in the long run," because the long run ends in you wrestling with Pandoc to try to get it to format things the way some particular conference requires. (True story: I submitted the outline for our upcoming SIGCSE workshop to the ACM using their LaTeX template. During the holiday break, I got mail telling me I had to re-do it using their MICROSOFT WORD template (their capitalization), which of course LibreOffice couldn't load properly.) So: given that the end product must be acceptable to senior profs and journals, and that markup-based tools impose more cognitive load on newcomers than WYSIWYG alternatives (i.e., the payoff for switching is tomorrow, the pain is today), what's our path forward? What can we teach in an hour that the average biologist will find compelling?

The last question is the most important. Everybody's deadline is tomorrow or next week; the hours they spend today learning something that might pay off in the long run increase the risk of them not meeting that near-term deadline (and the risk that their supervisor will ask them to re-do it because what's GitHub?).

But Jon Pipitone (who works in a research hospital) disagreed:

Even if folks are writing their papers in Word, I still think version control is a useful tool when paper writing, because there is so much more to writing a paper than just the final document, e.g., results files, figures, images, correspondence, submission documents, as well as any scripts you use to do analysis and generate other assets. You may not be able to use git diff on a Word doc but you can use it on many of these other things. And even then, under version control you can still checkout an older copy of your paper, and use Word's compare feature to do the diff. Plus you get the benefits of having a log of your changes, easy backups (e.g., git push) and rollbacks, etc.

The point I'm making is I think the benefits of version control when paper writing are worthwhile despite the fact that Word files don't diff easily. I'd also like to suggest that teaching folks to use knitr or IPython Notebooks or even just to create scripts to generate figures) can be a really useful thing. I've been showing people how to use RStudio to create a draft of their paper in Markdown to leverage the power of knitr. Even those that don't draft their paper in Markdown but just use it like an IPython Notebook get value out of being able to build up a document of figures and tables which they can paste into their word documents.

Cameron Neylon then tried to refocus the discussion on this key point:

We need a framework to discuss this in that steps a little away from the framework of the rest of Software Carpentry. The reason I say this is actually well demonstrated by the subtle ways in which all the suggestions are butting up against each other in not so comfortable ways. All of us have an implicit framework into which our thinking about authoring and sharing papers fits. Many of us also have a similar, but perhaps not identical, framework we use to think about code (and data, and... and...)

The students don't.

They're just at the point of trying to wrap their head around version control and the shell. That means to my mind... that a combination of the practical and the abstract will help them understand both the software side better as well as allow them to come to their own conclusions about how that framework does or does not apply to authoring papers.

Or to put it more simply: You've just learned about some ways of thinking about writing and using code and data that might help you work better. Authoring a paper is a different process. Here's why. Maybe it doesn't need to be...or maybe it does. What do you think? What will work for you? And do you now understand why version control is such a fantastic thing?

Ian Mulvany then contributed a lengthy comment, which he later turned into a detailed, insightful blog post. The whole thing merits close reading, but his key recommendations are:

  1. Use a reference management tool.
  2. Find the fastest venue to publish in.
  3. Publish in an open access journal.
  4. Add your work to the best preprint server for your discipline (and possibly a university archive).
  5. Add as much supporting material as you can to the right locations, e.g., github for code, vimeo or you tube for videos, and figshare for almost anything.
  6. Register for an ORCID and add your publication to your ORCID profile.
  7. Don't be afraid to alter publishers' copyright transfer statements.
  8. Use version control.
  9. Don't waste time formatting your paper (especially your references), because it will all be thrown away by the publisher.
  10. If the collaborative environment of your choice is not working for your group, drop it and get the damn paper finished.

There's a lot here to digest, but I now believe that Software Carpentry should introduce bootcamp participants to new ideas in scientific publishing. I believe we can as well, i.e., that the tools and practices people like Justin, Cameron, Carl, Jon, and Ian use are now within reach of our learners (if only just). If you'd like to help us work out the specifics—in particular, if you'd like to help us create an hour-long teaching module on 21st Century scientific publishing—please join the discussion.

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