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Saturday, August 29, 2020

Computable figures. eLife's Executable Research Article

When I did my PhD and wrote my articles, Ron Wehrens introduced me to R as open source alternative to MatLab which was the standard in the research group otherwise. At some point, I got tired of making new plots, and I started saving the R code to make the plot. I still have this under version control (not public; will be release 70 years after my death; I mean, that's still the industry standard at this moment </sarcasm>).

Anyway, I'm delighted that the published behind eLife keeps on innovating and introduced their Executable Research Article. The idea live figures still excited me very much and you can find many examples of that in my blog, and we actively use it in our Scholia project (full proposal). In fact, I still teach Maastricht University students this too, in the Maastricht Science Programme PRA3006 course.

I really wish we had something like this at BMC too, because I'm sure a good number of Journal of Cheminformatics authors would be excited with such functionality. This is their workflow:

Workflow of publishing an ERA in eLife. Image license: CC-BY, source.

One of the tools they mention is Stencila which I really need to look at in detail. It is the kind of Open Science infrastructure that universities should embrace. I'm also excited to see that citation.js is mentioned in the source code, one of the projects Lars Willighagen has been working on, see this publication.

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