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Protocols: The Devil is in the Details

Hopefully you know already about the PLOS partnership with protocols.io; if you don’t, PLOS announced this almost exactly a month ago. What we didn’t tell you then was that PLOS Biology had been trialling a pilot with some of our authors, working more closely with them to submit their relevant protocols to protocols.io, for a couple of months beforehand.

The authors who participated have been a delight to work with both from our side and with the folk at protocols.io.  We’re very pleased to already have two research articles published with the DOI links to their protocols embedded in their Materials and Methods sections [1,2], and another one will follow later this month.

Please take a few minutes to watch the video that provides a glimmer of the authors’ satisfaction at their experience with using protocols.io and also demonstrates just how easy it is to upload a protocol. The video includes snippets from the cofounder of protocols.io, Lenny Teytelman, and three early-adopting PLOS Biology authors— Zita Carvalho-Santos and Ana Patrícia Francisco, whose paper with Carlos Ribeiro and colleagues published on April 25th [2], and future PLOS Biology author Zoya Ignatova (whose paper will publish later this month – we’ll come back and add the citation later).

Why Upload Protocols?

A very common stumbling block in any discipline is difficulty reproducing something that someone who isn’t around anymore did from just their scribbled notes. Be it your Grandma’s shortcrust pastry (she wasn’t much of a cook, but wow could she make amazing pastry), or how that legendary “green-fingered” post-doc in the lab before you managed to get a complex multi-step, 3 week-long, tricky experiment to work (you know, the experiment that has been reduced to two sentences in the resulting research article’s materials and methods). Frustration at Grandma’s horrendous hand-writing/your former lab-mate’s scribbles, or the lack of detailed instructions on water temperature or how long to mix for—things critical to a successful outcome—are likely to run high. How on earth did they make it work!?

Precision is key—whether for a tricky recipe or lab experiment—and materials and methods generally don’t include sufficient detail for replication (nor should they, as a stepwise description makes for poor narrative). But we need to know those details—the devil is in them after all. Remember the unit error (English rather than metric) that led to the loss of a $125 million NASA Mars probe in 1999 [3]? Or when around 2000 trains were made too wide for the regional platforms in France in 2014 [4]. These are just two examples where measurements were key and mistakes were very costly. The details of quantities, concentrations and units are of utmost importance for a successful experiment, and errors—or failure to pass along sufficient precise info—can also be very costly for science.

The protocols.io link in a recent PLOS Biology paper (left) and the corresponding entry in protocols.io (right) 10.1371/journal.pbio.2000931

And this is why uploading your protocols to protocols.io (or something equivalent) is ideal; you’ll record and preserve all of the minute details. They’ll be available for others to replicate both within your lab or by others (possibly even by yourself—perhaps reading your own scribbled lab notebook is not only a challenge to others).You’ll get kudos for doing so as the protocols will be independently citeable. What’s more, they’re not static: follow-up comments, discussions, and tweaks to the methods can also be captured and made available.

As you go through the editorial process to publish your manuscript in any PLOS journal  you’ll be encouraged to upload any and all relevant protocols to protocols.io. Please watch the video to see for yourselves how easy this is to do. And please then upload your protocols!

Featured Image: An alchemist in his laboratory with his family: to the right they are shown calling at the poorhouse, destitute after the husband’s obsessive, fruitless experiments. Credit: Pieter Bruegel via Jeronimus Cock and Wikimedia Commons


  1. A Ca2+channel differentially regulates Clathrin-mediated and activity-dependent bulk endocytosis 
    Yao CK, Liu YT, Lee IC, Wang YT, Wu PY (2017) A Ca2+ channel differentially regulates Clathrin-mediated and activity-dependent bulk endocytosis. PLOS Biology 15(4): e2000931. https://doi.org/10.1371/journal.pbio.2000931
  2. Commensal bacteria and essential amino acids control food choice behavior and reproduction
    Leitão-Gonçalves R, Carvalho-Santos Z, Francisco AP, Fioreze GT, Anjos M, et al. (2017) Commensal bacteria and essential amino acids control food choice behavior and reproduction. PLOS Biology 15(4): e2000862. https://doi.org/10.1371/journal.pbio.2000862
  3. https://en.wikipedia.org/wiki/Mars_Climate_Orbiter
  4. http://www.europe1.fr/economie/les-nouveaux-ter-sont-trop-larges-pour-les-quais-2127287




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