Interactive Authoring Environments for Reproducible Media: Stencila

One of the problems associated with keeping up with tech is that a lot of things that “make sense” are not the result of the introduction or availability of a new tool or application in and of itself, but in the way that it might make a new combination of tools possible that support a complete end to end workflow or that can be used to reengineer (a large part of) an existing workflow.

In the OU, it’s probably fair to say that the document workflow associated with creating course materials has its issues. I’m still keen to explore how a Jupyter notebook or Rmd workflow would work, particularly if the authored documents included recipes for embedded media objects such as diagrams, items retrieved from a third party API, or rendered from a source representation or recipe.

One “obvious” problem is that the Jupyter notebook or RStudio Rmd editor is “too hard” to work with (that is, it’s not Word).

A few days ago I saw a tweet mentioning the use of Stencila with Binderhub. Stencila? Apparently, *”[a]n open source office suite for reproducible research”. From the blurb:

[T]oday’s tools for reproducible research can be intimidating – especially if you’re not a coder. Stencila make reproducible research more accessible with the intuitive word processor and spreadsheet interfaces that you and your colleagues are already used to.

That sounds appropriate… It’s available as a desktop app, but courtesy of minrk/jupyter-dar (I think?), it runs on binderhub and can be accessed via a browser too:

 

You can try it here.

As with Jupyter notebooks, you can edit and run code cells, as well as authoring text. But the UI is smoother than in Jupyter notebooks.

(This is one of the things I don’t understand about colleagues’ attitude towards emerging tech projects: they look at today’s UX and think that’s it, because that’s how it is inside an organisation – you take what you’re given and it stays the same for decades. In a living project, stuff tends to get better if it’s being used and there are issues with it…)

The Jupyter-Dar strapline pitches “Jupyter + DAR compatibility exploration for running Stencila on binder”. Hmm. DAR? That’s also new to me:

Dar stands for (Reproducible) Document Archive and specifies a virtual file format that holds multiple digital documents, complete with images and other assets. A Dar consists of a manifest file (manifest.xml) that describes the contents.

…

Dar is being designed for storing reproducible research publications, but the underlying concepts are suitable for any kind of digital publications that can be bundled together with their assets.

Repo: [substance/dar](https://github.com/substance/dar)

Sounds interesting. And which reminds me: how’s OpenCreate coming along, I wonder? (My permissions appear to have been revoked again; or the URL has changed.)

PS seems like there’s more activity in the “pure web” notebook application world. Hot on the heels of Mike Bostock’s Observable notebooks (rationale) comes iodide, “[a] frictionless portable notebook-style interface for literate scientific computing in the browser” (examples).

I don’t know if these things just require you to use Javascript, or whether they can also embed things like Brython.

I’m not sure I fully get the js/browser notebooks yet? I like the richer extensibility of things like Jupyter in terms of arbitrary language/kernel availability, though I suppose the web notebooks might be able to hook into other kernels using similar mechanics to those used by things like Thebelab?

I guess one advantage is that you can do stuff on a Chromebook, and without a network connection if you cache all the required JS packages locally? Although with new ChromeOS offering support for Linux – and hence, Docker containers – natively, Chromebooks could get a whole lot more exciting over the next few months. From what I can tell, corsvm looks like a ChromeOS native equivalent to something like Virtualbox (with an equivalent of Guest Additions?). It’ll be interesting how well things like audio works? Reports suggest that graphical UIs will work, presumably using some sort of native X11 support rather than noVNC, so now could be a good time to start looking out for souped up Pixelbook…

PS March 2019 – Stencila desktop appears to have stalled for some time. As it’s built on the Texture wordprocessor / editor, it may end up as a plugin for that…

PPS June 2021 – have things rebooted again for Stencila? https://elifesciences.org/labs/a04d2b80/announcing-the-next-phase-of-executable-research-articles