protocols.io

dynamic and interactive research protocols with community review

In a nutshell

The mission of protocols.io. is to make it easy to share method details before, during, and after publication.

Published research protocols get community annotation on protocol- and step-level. Authors often improve the originals based on this feedback, easily creating updated versions with a few clicks.

Goals and intentions

The protocols.io platform was inspired by the frustration of one of the co-founders regarding lack of a central space to share corrections and optimizations of previously-published methods.

After launching, the team behind protocols.io realized that most research papers do not contain adequate descriptions of the methods. So the mission of the company evolved into encouraging culture change towards better reporting of the details upon publication and then enabling scientists to keep the methods up-to-date.

Types of outputs

Other scholarly outputs

Review process

Review requested by

Non-authors
Reviewer selected by

Self-nominated
Public interaction

Yes
Author response

Yes
Decision

None

Review policy

Review coverage

Specific aspects
Reviewer identity known to

Editor or service
Competing interests

Not included

Social Networks

Video

Review features

Notes

Handled by competent reviewers with good editors, pre-publication peer review improves the submitted papers. However, improving quality is not the same as ensuring it. A typical reviewer is unlikely to verify the scripts and rerun analyses reported in a genomics paper. Similarly, it would be highly unusual for a reviewer of an experimental molecular biology paper to dash to the lab and attempt to reproduce the reported results as part of checking the paper.

The peer review that can truly verify any given paper is the gradual process of replication and extension of the published work over time. When authors of a given paper or other researchers follow up on a publication – then and only then – do we really catch mistakes, improve, and verify the work. This is why it is so important to report not only the results, but the code, data, and the detailed methods used to produce these results. This is why the efforts of publishers like GigaScience are so important.

We were driven to create protocols.io by the desire to establish a central place where scientists can share and discover optimizations and corrections of published methods; our hope is that through versioning and collaborative sharing post-publication, methods can evolve and remain up-to-date, long after the original publication.

Excellent example of such community review:

https://www.protocols.io/view/cut-run-targeted-in-situ-genome-wide-profiling-wit-mgjc3un
Eligible reviewers/editors

Any registered user is allowed to comment.
Tags or badges

Yes
Criteria for inclusion

We try to expose all possible metrics that may be helpful in assessing whether a protocol is likely to work. Each public protocol has a dedicated "metrics" tab with this information.

Example: https://www.protocols.io/view/cut-run-targeted-in-situ-genome-wide-profiling-wit-mgjc3un/metrics
Explanation of cost

The protocols.io platform is free to read and share for public content. For private collaboration, there is a limit of 5 free private protocols per user, requiring a $5/month subscription above that.