Doubling down on Markdown for science
Scientific authoring workflow is a beast. You keep notes on paper (hopefully, a notebook, and not just loose pages), in word-processing documents unhelpfully named “notes” followed by “notes1,” “notes2” or worse, “notes_old,” “notes_old1.” You manage your bibliography on your desktop or on the web, you have a directory folder full of images, charts, photos and other media, and you collaborate with your co-authors by emailing attachments back and forth.
Sooner or later you start doubting your sanity but you soldier on. Finally you publish your paper, heave a sigh of relief, and move on, thereby ensuring your data can’t be reused and your work can’t be reproduced easily.
Several coders, designers, scientists, and publishers met at PLOS to brainstorm toward a better, more modern way. The Markdown for Science workshop was organized by Martin Fenner and Stian Håklev and supported by a 1K Challenge Grant from FORCE11.
While a lot of good ideas were generated, we have a long way to go. Keep an eye on this project, and better yet, pitch in with your ideas and code. Together we can tame this beast.