protocols.io

What is protocols.io?

The protocols.io platform is a free and open access repository for recording and sharing detailed up-to-date research methods and protocols. It allows researchers to easily create, edit, share, and get credit for their protocols, and provides an open access hub for scientists to communicate improvements and corrections to scientific methods.

The platform is useful for researchers in any discipline that uses a step-by-step methodology, such as biology, life science fields, medical science, health science, chemistry, neuroscience, engineering, data science, and computational science.

Introduction in protocols.io

Here you can find the recording of the webinar "Introducing protocls.io to researchers from BIH and Charité".

To the recording

Features

protocols.io's editor provides a structured way to create and modify a protocol in minutes. They can be made from scratch or uploaded and easily converted from an existing Word or PDF document.

Protocols and changes to them can be published for everyone to see or shared with selected private groups or individuals. Updates to protocols can be captured in new versions. Publicly published protocols can be assigned DOIs, which are then easily discoverable and citable in your publication or independently as a separate research output.

You can find more information about the features of protocols.io here.

Eligibility

The BIH QUEST Center provides this service for students, faculty and staff of the BIH and the Charité initially for 2 years (until 31.12.2024).

If a protocols.io account is created with a "charite.de" or "bih-charite.de" email address, premium features are activated automatically after account creation and confirmation via number code sent to the email address.

For existing protocols.io accounts with these affiliations, premium features are activated automatically. (It is also possible to upgrade an existing account made with a non charité associated email by validating using a Charité email.) See FAQ below.

Premium access

Premium access provides you with:

Unlimited private repositories
One-on-one training from protocols.io staff
Possibility to create a private or open workspace with up to nine Non-Charité/BIH members
Possibility to import of one existing protocol onto the protocols.io platform
- Submit a PDF of one protocol that you or your lab already have and the protocols.io staff editors will convert it into a protocol for you! How to submit an existing protocol for conversion (video 1:28)
Dedicated account & customer service with 24-hour turnaround
Audit trail and electronic signature for 21 CFR Part 11

Benefits

Protocols are dynamic and interactive, helping with collaboration within a group or among co-authors outside of the university
Continuous improvement and development: Users with access to a protocol can update, annotate, copy or fork it
Research groups can organise and archive their methods ensuring that knowledge is not lost as trainees move on
You can create different levels of access for any protocol
Interoperability with GitHub, OSF, RSpace, SciNote, and LabArchives
protocols.io renders in most browsers and devices – no apps or plugins needed. You can run the protocol step-by-step alongside your experiment, save a run record, and safeguard it
Connect your protocols.io account with your ORCID and information about your published protocols are automatically posted onto the Works section of your ORCID record
Citing your published protocol in your publication can significantly shorten your method section, which then focuses on the broader level of applied methodology
Receive and provide feedback via endorsement (Works for me) and commenting on steps
Run mode permits to execute an entire protocol as checklist alongside your experiment so you know when each step was completed (https://www.protocols.io/help/run)

Introduction to protocols.io [video 03:19]
Create a new protocol [video 01:34]
Create a new private protocol [step-by-step guide]
How to bring structure to your research with protocols.io [video 19:31]
Developing protocols with protocols.io [video 24:12]
Exporting protocols and files [video 00:51]
Publishing protocols [video 01:25]
Publishing a Lab Protocol paper with PLOS ONE and protocols.io [video 1:00:13]
Creating a new version of a protocol [video 01:23]
Running protocols [video 01:35]
Create a new group/lab workspace [video 00:31]

Who can see my protocols?
Private protocols are only accessible to the creator and whoever the creator chooses to give access to. protocols.io will only access your protocols when asked to do so. Shared protocols in private workspaces cannot be accessed or shared outside the group by anyone else.
What happens when I update my published protocol that I linked with a DOI in a publication?
Often protocols evolve further or need smaller corrections and adjustments, requiring creation of a new public version. Users accessing the protocol via the publication will be presented with to the older version together a with notification that a newer version of this protocol exists.
What happens to private protocols and the ones in private workspaces if the contract with protocols.io is not prolonged?
If the contract is not prolonged, users will continue to have access to their private protocols but will but will not be able to create additional private protocols if they have 5 or more protocols already. Users or groups that wish to continue using premium services can opt for their own subscription.
Who really has the copyright for a certain method?
Can I enter previously published methods? Yes, you can. Recipes and cookbooks are not subject to copyright. They are statements of fact/instructions, and therefore protocol steps and materials can be republished outside of the original journal. (However, please don't include direct copies of figures, tables, discussion, etc. from published articles - unless the article is fully open access with a CC-BY license, as this would be a breach of copyright.)
If you build upon, repurpose, and/or reuse text from a published protocol or research article, please ensure that you cite and attribute correctly all original source documents. If protocols.io becomes aware of overlap with any previously published work that has not been attributed, the author will be contacted with the request to include the citation in a new version.
I am a Charité/BIH member and I have an existing protocols.io account registered with a different email address. How can I benefit from premium service?
You can change your primary email address in the protocols.io settings and need to verify this in the email you receive from protocols.io. Alternatively, you click the “Upgrade Now” Button and click on “Academia” in the next window and select “Charité/BIH” from the organisation list. After provision of your Charité/BIH Email address and a verification step, you have Premium access as indicated in the upper left corner.
More Q&A: https://www.protocols.io/help/faq

Teaching: "Write and/or Publish My Protocol Working Group"

We offer a self-paced course to support scientists at various steps from protocol creation to protocol publishing. The course modules will help you to:

Plan and create a reusable step-by-step protocol
Share your protocol with colleagues locally and around the world by depositing it on protocols.io
Cite your shared protocol in the methods section of your papers
Prepare a Lab Protocols article describing novel methods that you have developed, to submit to PLOS One

Course videos can be viewed on YouTube. Each video will guide you through a step listed above. Course participants will interact with each other and with course instructors using MS Teams, and by joining biweekly working group sessions where participants can work on their protocols and get tips and feedback.

We will limit class sizes to ensure that participants have the opportunity to share and get feedback on their work in a small group setting.

More information and registration here.

Phone:	+49 30 450 539 706
E-mail:	rene.bernard@charite.de

What is protocols.io?

Features

Eligibility

Premium access

Benefits

Video tutorials

protocols.io FAQ

protocols.io 1.000 € Reward Program

Charité/BIH @protocols.io Collection

Dr. René Bernard