Category Archives: protocols

Facilitated Preprint Posting is now available for Lab Protocols at PLOS ONE

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Author: Marcel LaFlamme, Open Research Manager, PLOS

When authors submit a Lab Protocol to PLOS ONE, they prepare a short manuscript that contextualizes their step-by-step protocol, describing the value it adds to the published literature and providing evidence that the protocol works. This additional context helps readers to decide whether and, if so, how to adapt the protocol for their own research.

In 2023, PLOS is making it easier for authors to share these protocol manuscripts as preprints, by expanding our partnership with the preprint server bioRxiv to include Lab Protocols.

During the submission process, Lab Protocol authors will now be asked if they want PLOS to forward their manuscript to bioRxiv to be considered for public posting within a few days. Facilitated posting to bioRxiv has been offered at PLOS ONE since 2018. Extending this service to Lab Protocols means that authors can share and get credit for their methods development work sooner, even as the peer review process unfolds.

In keeping with PLOS ONE’s multidisciplinary scope, Lab Protocol submissions are welcomed from any scientific field. Through the end of 2022, 61% of submitted Lab Protocols were in the life sciences, making bioRxiv an especially suitable partner to promote their early sharing.

“bioRxiv has always encouraged authors to post new methods as preprints,” said Richard Sever, co-founder of bioRxiv. “Formats like Lab Protocols that put protocols in context and provide data supporting their use are a great way to make methods more discoverable, and we’re delighted to partner with PLOS to make these manuscripts immediately available to researchers.”

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Protocol entry service expanded to all Lab Protocol authors

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Author: Marcel LaFlamme, Open Research Manager, PLOS

When it comes to methods sharing, Lab Protocols at PLOS ONE offer researchers the best of both worlds: a platform specifically designed for step-by-step protocols, and a peer-reviewed publication in a well-regarded journal.

As of today, we are expanding a service offered to Lab Protocol authors through our partnership with protocols.io: the team at protocols.io will format step-by-step protocols for their platform at no charge and at any stage of the Lab Protocol writing or review process, even prior to submission.

This service will save time for PLOS ONE authors who may not be familiar with the rich functionality of the protocols.io platform, which includes features like timers, labels for critical steps, and the option to embed media objects like videos. The team at protocols.io can also provide feedback to help authors improve the protocol’s presentation, clarity, and reproducibility.

“One of the things I love about Lab Protocols is that they help researchers get credit for method development and publish sooner in their careers. Now, with the expansion of the protocol entry service, we are going a step further in making researchers’ lives easier. I am really excited about this expansion and believe that it is a unique offering in the protocol publishing space,” said Lenny Teytelman, CEO of protocols.io.

Previously, the protocol entry service was offered to Lab Protocol authors whose submissions had already been sent out for peer review. By expanding it to all current and future Lab Protocol authors, PLOS ONE is making it easier for authors to provide an optimized step-by-step protocol as part of their initial submission.

Authors also have complete control over how and when the protocol is made available at protocols.io. The newly formatted protocol will not be visible to anyone else until the author has been able to inspect it and make changes. Authors can then choose to share it publicly, or to generate a private link accessible only to PLOS ONE editors and reviewers. In the event that the Lab Protocol is not accepted at PLOS ONE, authors can still choose to share the step-by-step protocol on protocols.io for other researchers to use and build on.

Lab Protocol authors can access this free service by emailing plosone@plos.org to request a customer code, which will be provided in two to three business days. The author can then enter the code when submitting their step-by-step protocol to the protocol entry service.

“We are delighted that the team at protocols.io is now offering this service to all Lab Protocol authors. Helping authors make the most of the unique features of the protocols.io platform will ensure that the protocol is widely used, shared and further developed. This service is very much aligned with our goal of making the submission process as painless and straightforward for our authors as possible,” said Emily Chenette, Editor in Chief of PLOS ONE.

Image credit: protocols.io

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Do.abl.es

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Do.abl.es

Do.abl.es

Do you want to know you can measure DNA contour lengths using ImageJ?  Perhaps you want to stain a C. Elegans embryo for imaging?  Or possibly, you might want to test whether or not you have gotten an immune response using ELISA?

Martin Fitzpatrick sends word of a cool collection of open access scientific protocols called Do.abl.es.  For the uninitiated, protocols are the recipes that scientists use to carry out experiments in a reproducible way.  The list of protocols posted to Do.abl.es to date has a number of interesting and important biochemistry and biology experiments.

There’s also a neat companion site called Install.abl.es which concentrates on many of the same things we do – the use of open source software in the sciences.