Protocols.io: recipes for innovation in Open Science

Sometimes the most influential outcome of research is a method. Landmark papers on CRISPR gene editing1-3 provide one notable example of the impact methods can make on a field of science. But most articles do not have the method celebrated front and centre stage, and many journals will reject an article for being ‘just a methods paper’ and not having enough impact.

Yet almost every article in science has some sort of method a recipe which tells the story of how the researchers did what they did. Most go unsung and most, like the seminal CRISPR papers or another landmark method that also sparked controversy, the polymerase chain reaction (PCR), are themselves the culmination of years of work by many researchers in different locations working on very disparate topics4-6. Whenever a method is useful or intriguing, others will innovate. They will use it, challenge it (most recently Kosicki et al.7 in relation to CRISPR), refine it and adapt it that’s how science works.

Even when a method doesn’t hit the headlines8, it is still a crucial output of research that needs to be set out in enough detail to make the results and conclusions credible and enable others to re-use or adapt it if needed. Hindawi journals have no space restriction on methods, but the way research is communicated in most journals today often requires the methods section to be relegated to a supplementary file or made so concise that it is impossible for others to follow the recipe. And more often than not, the painstaking work that goes into developing or refining a method is never explicitly rewarded. In many cases, it is early career researchers who do much of the work9. This is why we are encouraging all our authors to not only outline their method in their manuscripts but to publish it independently of the paper as a separate creditable output of research and then cite it in their papers. There are a variety of platforms and repositories that enable this. We are partnering with one Open Access platform, protocols.io, to make it easy for authors to publish and adapt the methods they develop and get credit for them via a dedicated citation. Publishing your method not only helps to credit such outputs directly, it contributes to an open foundation of knowledge and is part of Open Science.

Creating your method on protocols.io and linking to it from your submitted article is straightforward (see the relevant journal guidelines and ‘How it works’ below) and has several benefits. You can create, develop, edit, and time your method in a structured way. You can work on it online together with colleagues, version it, choose to publish it at any time (with a CC BY licence), or make it privately available for editors and reviewers. It allows you to put in all the details and steps, including hints and tips that you don’t put in the final article, which enable others to follow your recipe. Other researchers can also copy and modify any protocol you make public, and can share this knowledge in a way that preserves credit for you the original authors.

Protocols are commonly used in clinical and laboratory research but ‘protocol’ covers any structured method and can apply to any discipline. On protocols.io there are currently published methods not just from the clinical sciences but also from ecology, computational science, and even the assembly of an autonomous reef monitoring structure.

A published protocol enhances the value, transparency, and credibility of your journal article. And because it is published independently with its own citation, you can cite the method not only in the first paper that uses it but in other relevant papers and elsewhere, saving you time (see the protocols.io FAQ page). Unlike the supplementary material of most journals, the methods on protoocols.io are also fully searchable, and they can be updated once published.

There is growing public concern about how much of science is trustworthy and several journals and publishers encourage or request authors to make their protocols available to readers alongside the article. Publishing your method and making it freely available for others to use gives others greater confidence in your work as well as letting you get dedicated credit for it.

Methods are in and of themselves building blocks of science a source of innovation. They are there as a record if others want to adopt the same approach or to check the validity of the results. Being able to reproduce a method accurately is also vital if you want to tinker with it or refine it. As the CRISPR story tells, methods can also be a source of real innovation, even when controversial or if the early steps don’t show the same promise.  

How it works

  1. Register at protocols.io and create your protocol
  2. Select ‘Get DOI’ on the protocols.io menu tab
  3. Include the DOI in the Methods section of your manuscript as follows (for any article in a Hindawi journal): http://dx.doi.org/10.1155/protocols.io.[PROTOCOL NUMBER]

Editors and reviewers can use the DOI link to view the protocol (instructions are also available on protocols.io). If your article is published, this referenced link will automatically make your protocol publicly available, enabling readers to view your detailed methods. The protocol will also be linked to your article on protocols.io.

You can also make your protocol public before publication of your article if you choose, which will not harm the peer-review process of your manuscript and you can link it subsequently to the publication. This may allow you to get comments about your methods to adapt or improve them before you submit your article to a journal.

References

  1. Jinek, Martin, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A. Doudna, and Emmanuelle Charpentier. “A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity.” Science 337, no. 6096 (August 17, 2012): 816–21. https://doi.org/10.1126/science.1225829.
  2. Cong, Le, F. Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D. Hsu, et al. “Multiplex Genome Engineering Using CRISPR/Cas Systems.” Science (New York, N.Y.) 339, no. 6121 (February 15, 2013): 819–23. https://doi.org/10.1126/science.1231143.
  3. Mali, Prashant, Luhan Yang, Kevin M. Esvelt, John Aach, Marc Guell, James E. DiCarlo, Julie E. Norville, and George M. Church. “RNA-Guided Human Genome Engineering via Cas9.” Science (New York, N.Y.) 339, no. 6121 (February 15, 2013): 823–26. https://doi.org/10.1126/science.1232033.
  4. Zhang, Sarah. “The Battle Over Genome Editing Gets Science All Wrong.” Wired, October 4, 2015. https://www.wired.com/2015/10/battle-genome-editing-gets-science-wrong/.
  5. Bartlett, John M. S., and David Stirling. “A Short History of the Polymerase Chain Reaction.” In PCR Protocols, 3–6. Methods in Molecular BiologyTM. Humana Press, 2003. https://doi.org/10.1385/1-59259-384-4:3.
  6. “History of Polymerase Chain Reaction.” Wikipedia, April 24, 2018. https://en.wikipedia.org/w/index.php?title=History_of_polymerase_chain_reaction&oldid=838056328.
  7. Kosicki, Michael, Kärt Tomberg, and Allan Bradley. “Repair of Double-Strand Breaks Induced by CRISPR–Cas9 Leads to Large Deletions and Complex Rearrangements.” Nature Biotechnology 36, no. 8 (August 2018): 765–71. https://doi.org/10.1038/nbt.4192.
  8. Corbyn, Zoë. “Crispr: Is It a Good Idea to ‘Upgrade’ Our DNA?” The Observer, May 10, 2015, sec. Science. https://www.theguardian.com/science/2015/may/10/crispr-genome-editing-dna-upgrade-technology-genetic-disease.
  9. Ledford, Heidi. “The Unsung Heroes of CRISPR.” Nature News 535, no. 7612 (July 21, 2016): 342. https://doi.org/10.1038/535342a.

Catriona MacCallum is Director of Open Science at Hindawi.

The text in this blog post is by Catriona MacCallum. It is distributed under the Creative Commons Attribution License (CC-BY). The illustration is by Hindawi and is also CC-BY.