Online / 6 & 7 February 2021

schedule

Emacs and org-mode for reproducible research

Organize your research in plain text!


This presentation illustrates how the GNU Emacs text editor provides an powerful integrated environment for reproducible research, effectively bypassing the need for juggling different software in order to write and execute code, manage data or write papers. GNU Emacs as a long history, and is still widely used and supported by a very active community of users and developers. A very popular feature of GNU Emacs is Org-mode which, at its core, offers a markup language similar to Markdown.

Following a brief introduction to Org-mode, this presentation demonstrates its use for reproducible research: straightforward mixing of prose and code, execution of code blocks as well as display of the results. With Org-mode, GNU Emacs is turned into a computational notebook which functionalities goes well beyond popular alternatives such as Jupyter. Code blocks are not restricted to a particular programming language and data can be passed between them: generate data in C, analyse it in Python, visualise it with R, all in one single executable document. Moreover, Org-mode documents are nothing but plain text, making them inherently portable, sustainable, and suited to version control - crucial qualities for academic research. Moving on, I illustrate the export of Org-mode documents to richer formats: PDF, ODT, HTML and many more - all from within GNU Emacs. Lastly, I broaden the scope of this presentation and discuss the open nature of GNU Emacs itself. Indeed, GNU Emacs is free (as in freedom) software under a copyleft license. This ensures that GNU Emacs remains sustainable, community-owned software: GNU Emacs will never be "discontinued" or its features reduced inside a "community edition".

If GNU Emacs is widely used among GNU/Linux users, it is a rather unusual component of nowadays researchers' toolbox. This presentation is an opportunity for attendees to (re)discover GNU Emacs, not so much as a code editor, but as a powerful tool for reproducible research, from day-to-day data collection and analysis, all the way to paper publication. Despite being over 30 years old, GNU Emacs comes with with very modern ideas, highly relevant to today's discussions of openness and reproducibility in scientific research. Beyond the tool itself, this presentation is an opportunity to sparkle discussions on the nature of research tooling. GNU Emacs has always been developed and maintained in the open, and its license ensures that it will always be. GNU Emacs maintenance and development is a collective, not-for-profit effort of thousands of developers worldwide and anyone wanting to make modifications to it is welcome to do so. This ensures both reliability and sustainability, which are key characteristics for any tool at the core of a reproducible research practice.

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Photo of Thibault Lestang Thibault Lestang

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