Last Friday 23rd June, researchers at the Barcelona Biomedical Research Park (PRBB) had a chance to find out more about protocols.io, an open-access platform for researchers to collaboratively create step-by-step, interactive and dynamic protocols.
In this platform, researchers can privately share protocols with specific colleagues or make them public to the whole scientific community with ease and efficiency. Also, according to the company, “real-time communication and interaction keep protocols up to date with versioning, forking/copying, Q&A, and troubleshooting. Public protocols receive a DOI and allow open communication with authors and researchers to encourage efficient experimentation and reproducibility”.
The session by Gabriel Gasque, Head of Outreach of protocols.io, was hosted by Daniel Richter – researcher at Institute for Evolutionary Biology (IBE: CSIC-UPF) and early user of the platform – and supported by the PRBB Good Scientific Practice working group.
We took the chance to interview Gasque to learn more about this initiative.
To know more, you can also check Gasque’s presentation here.
When did protocols.io first appear and why?
It was a created in 2014 by Lenny Teytelman, Irina Makkaveeva and Alexei Stoliartchouk. Lenny– a scientist – found that he had been working for 2 years painstakingly solving an error in a methodology – to be rewarded by it only with a sentence in the Materials and Methods section… Aware of the crucial importance of methods in research, he wanted to improve credit for method development, and thus created protocols.io. Here each published protocol has a DOI and can be properly referenced and credited.
That was of course just one side of the coin. The benefits of sharing protocols go beyond just getting credit:
- It increases discoverability and therefore use of the protocols or methods
- It ensures preservation, since all content is mirrored and backed up in several sites such as GitHub.
- It increases collaboration.
- It saves time (no need to rewrite the methods section every time, trying to be innovative in the way you describe it… just add a hyperlink to the detailed description in protocols.io)
- It ensures compliance with Spanish and European current recommendations regarding open science, data management, availability, etc.
- It increases reproducibility – as we all know, the great majority of materials and methods sections in papers don’t include enough information to understand, let alone reproduce, the results…
“Protocols published in protocols.io get a persistent identifies (DOI) so they can be easily credited, found, preserved”
Who uses it, and how much does it cost?
protocols.io is a for-profit company , but it is free to both post public protocols and to look for protocols and read and use them. All the public content is open access with a CC-BY license. There is a premium side to the platform (pricing at this link, which can be achieved through an institutional membership) that allows to have private workspaces, where you can have protocols that are not open to all – they are kept private for you or for a chosen group of collaborators. Many companies use this, for example.
Currently, we have over 155,000 registered users who have uploaded over 14,000 public protocols and more than 60,000 private ones. But in fact, we have more than 2,5 million visits a year to the protocols in our platform!
Regarding disciplines, it is a bit biased towards wet lab / biomedicine protocols, although they also have some from archaeology, social sciences, computational biology, or ecology… Also, some users use us to ‘preregister’ their clinical trials, by publishing the protocol here before it starts.
How is the interaction with journals – isn’t it a problem to publish methods in protocols.io if they have been published in a paper?
It’s not! In fact, more than 500 journals and several funders promote the use of protocols.io. Also, the content of a recipe is not copyrightable. You can’t post it exactly as it is in the journal, with the same format etc., but you can republish the content and steps of any methodological recipe.
In many cases, authors publish a paper with their research results, and in the “Methods” section they link to the detailed method in protocols.io. This has several advantages.
On the one hand, the protocols in our platform are dynamic, which means there can be newer improved versions – each with its own DOI, because once a protocol is published it cannot be changed. So, from the paper, you will go to the original method, the one used in the article; but the platform will tell you if there is an updated one if you want to check it. And it also allows you to compare both versions to see what changed.
Another advantage is that by publishing a method independently of a paper, you make it more discoverable and reusable; for example, a method used in a paper about fish parasites can be useful for someone working on mouse neurons. But the neuroscientist is unlikely to check the fish paper… however they can find the protocol in our platform if they search for the right keywords.
By publishing a method independently of a paper, you make it more discoverable and reusable. Also, the protocols are dynamic and can be updated.
How can people use the protocols?
The protocols are step-by-step recipes, very detailed and very clear, color-coded. You can just read them or download them to have them at hand while doing the experiment. You can make your own copy, where you can mark what have you done, or comment on any step where you have done something different, e.g., so you keep a copy of your specific experiment. Or you can create your own protocol based on another one, and adapt it to your model, conditions, etc. In this case, your new ‘forked’ protocol will be clearly linked to the original one, so the credit line is maintained.
And how can someone upload an existing protocol?
There are three ways – with three levels of ‘effort’, but all of them very easy, really!
You can just drag your protocol (in word or whatever) into your workspace in protocols.io. Note, though, that this won’t be ‘publishable’: it cannot be published to receive a DOI and it won’t be open for everyone else to see. It’s just a way to keep all your protocols together.
To publish it, you must do it via the editor in the platform. But again, you can do it in a very simple way – you create an empty protocol, add a title and summary, and then attach the protocol as a word or PDF document. This can be published, have a DOI and be public, but it won’t be dynamic.
The third, more complex way, is to copy-paste each step, as a bullet point text. Then the platform transforms it into a dynamic protocol, with the right format that can be copied, forked, etc.
Even this complex option is not complicated, although of course it takes a bit more time… We also have an import service that does this for a fee.