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Author: Mericka McCabe

Associate Scientific Engagement Manager

Whatever your research topic, the step-by-step methods behind your study are key to understanding your results. These protocols may be detailed instructions for a specific experiment or synthesis, day-to-day lab/field instructions, computational workflows, or the broader methodological framework used to answer a research question. Sharing them openly helps others understand what you did and what they would need to do to reproduce, verify, or build on your work. It also helps you meet the open science expectations of funders and publishers. Building on our previous introduction to sharing protocols, this guide covers how to prepare, publish, license and cite your protocols so they’re easy to find, use, and receive credit for.

Why best practices matter

Sharing detailed protocols openly enables clarity, usability, and reproducibility, so that others can follow your methods without guesswork. Recording your complete methods in an accessible format addresses many common pain points:

• Reduce guesswork by replacing vague or missing steps with precise instructions.  
• Enhance reproducibility by surfacing dependencies (such as reagents, equipment, or software and their versions, where relevant). 
• Provide clarity by stating exact conditions (e.g. timings, temperatures, or acceptance ranges when those matter). 
• Ensure readability by avoiding jargon and using plain, defined terms. 
• Prevent dead ends by including expected outcomes and simple troubleshooting. 

By clearly recording your methods, you make it easier for anyone trying to replicate or build on your work, including your future self. Sharing protocols also helps to contextualise results so that others may accurately interpret and reuse your data. 

Benefits of sharing your detailed protocols openly:

• Reproducible results: complete steps, conditions, and materials let others (and your future self) repeat your work. 
• Faster peer review: clear methods reduce back-and-forth with editors and reviewers. 
• Compliance: many funders, institutions, and journals encourage or require accessible, reusable methods. 
• Reuse & recognition: modular, self-contained, and citable protocols can be discovered, reused, and properly credited. 
• Future proofing for your own work: versioned, well-documented methods save you time later and remove uncertainty as your protocol is adapted. 
• Community benefits: sharing methods for others to build on advances science for all. 

Step one: prepare your protocol for open sharing

- Write in clear language: keep instructions in active voice (e.g. instead of “a 25 µl reaction was set up containing” write: “set up a 25 µl reaction containing”), define all acronyms, and write each step as plainly as you can. 

- Make it complete: it should be possible to follow each step you took, using the same resources that you used. 

• Cover the essentials: list all materials, equipment, and resources you used (e.g. reagents/instruments, datasets/archives, analytical tools) with supplier, model, lot/batch numbers, and RRIDs, where relevant. Include recipes and detailed parameters (e.g., buffer recipes; corpus selection rules) and software versions.  
• Write the steps in chronological order: for each step, include the conditions that matter for your field (e.g. time, temperature, voltage, sampling rate, thresholds) and the expected output or critical points, if relevant.  
• Provide guidance: note any expertise required, safety information, ethics notes, limitations, and references (see also PRO-MaP’s protocol reporting checklist). 

- Add context:  

• Write for discoverability: give your protocol a precise and searchable name and include a 3-4 sentence abstract that explains what it does, when to use it, and the expected outcome. Be sure to add relevant keywords. 
• Provide tips: consider additional points that would help someone repeat the method; for example, troubleshooting tips and visuals, such as short instructional videos or images for critical steps. 

- Give credit: ensure all authors involved in developing the protocol are properly credited, apply similar criteria as you would to determining authors on a research manuscript. Authorship order on a protocol often differs from an associated manuscript, ensuring appropriate credit for specific outputs. 

- Seek feedback: ask others from your group, department, or  chosen collaborators to review the complete protocol. 

Step two: choose the right platform  

We encourage authors to share protocols on a dynamic protocol platform of their choice, such as . Unlike a static word or PDF file, these platforms may: 

• Allow you to structure your method in a step-by-step format that’s easy to follow. 
• Provide a DOI so your protocol is citable and findable. 
• Enable version control. 
• Integrate with tools you already use, such as Electronic Lab Notebooks (ELNs), cloud storage servers, and some journal submission systems. 

Step three: ensure long-term accessibility  

Think of a protocol as a brief, modular, and self-contained scientific publication. With a DOI-minting repository like protocols.io, readers can retrieve the exact version of your method years later, while still enabling you to update the protocol with separate versions as your method evolves over time.  

• Label your version, to keep a clear log of what has changed over time and why. Ensure that each version has its own DOI. 
• Cite your protocol: add the protocol DOI to the Methods section and include a citation in the References list to ensure accessibility. 

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A licence tells others exactly what they may do with your protocol, and under what conditions.   

• Select a  for maximum reuse potential (this is the default when publishing on protocols.io). 
• Determine if your protocol repository of choice has licensing terms  
• Check if your funder mandates the use of a specific licence.  
• If your protocol uses any third-party content, check whether you have permission to include them under your chosen licence and ensure the content is properly credited. 
• Ensure that the licence information is included in the protocol record. 

Step five: ethical and legal considerations  

Like with other research outputs, it’s important to share protocols responsibly. 

• Protect participants and IP: remove confidential or identifying information (e.g. patient IDs, GPS coordinates to sensitive sites, proprietary formulas, trade secrets, security keys, or identifiable photos of people). 
• If removing details affects a step, say so briefly and explain how readers can proceed (e.g. use of synthetic data, or controlled access). 
• Check compliance with funder, institutional, and journal policies: some studies must follow specific reporting standards (e.g. MDAR, ARRIVE, CONSORT, PRISMA, field-specific checklists). Link to these in your protocol record where relevant. 

Quick checklist for authors

If you keep these checks in mind as you work through your research project, you’ll be ready to share your protocols openly and be fully aligned with best practices and ���ϳԹ���’s policy expectations. 

1. Protocol is complete and clear  
2. Context (title, abstract, keywords) and troubleshooting included 
3. All authors are properly credited 
4. Dynamic protocols repository chosen and DOI assigned 
5. Creative Commons licence added 
6. Versioning and change log started  
7. Protocol DOI cited in any associated manuscript (in both Methods and References) 
8. Funders acknowledged and references used to develop the protocol cited, if applicable. 

If you’re interested in learning more about sharing your protocols,  hosts regular  on why and how to share detailed protocols. And read more about why sharing protocols and methods matters. 

Additional resources

• Blog post: Supporting open science practices: Why sharing protocols matters 
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•  (Nature) 
• Blog post: Protocols in practice: Benefits of the protocols.io platform for a public health laboratory network 
• Blog post: Improving research reproducibility with open method sharing 
•  (Nature) 
•  (Nature collection)