What are methods and protocols?
A protocol is a document that describes how a clinical trial or research project is conducted. It provides a detailed study design or set of instructions for carrying out a specific experimental procedure and is an essential tool for ensuring the validity and reproducibility of research results.
- A research method can be described as the approach used to examine a research question.
- A research protocol is the step-by-step process for producing results using the chosen method.
- A clinical protocol is a document that describes how a clinical trial will be conducted and how the safety of the trial subjects and the integrity of the data will be protected.
Protocols can also be written for computational workflows, operational procedures, safety checklists, and similar use cases.
Developing and publishing protocols
- Clinical Trial Protocol Development (UCSF’s Clinical Research Resource HUB) offers several protocol templates and related resources. Cancer Center templates and resources are also available.
- ClinicalTrials.gov Protocol Registration & Results System (PRS) or another appropriate registry is required for publication of clinical trial results in many journals.
- Evidence synthesis protocol development (Cornell University Library)
- OSF Registries (Center for Open Science) is a free platform for publicly registering study plans and protocols for qualitative research, evidence synthesis research, and Registered Reports. See support documentation and the guide to choosing the right template.
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protocols.io platform (Springer Nature; includes the former Protocol Exchange) for developing and sharing research protocols, which may be kept private or be published under an open access license with a DOI.
- UCSF’s premium account allows unlimited private protocols and workspaces.
- Integrates with several electronic lab notebooks (ELN).
- See a video on adding ELN records, and note UCSF's Guidance for Electronic and Paper Lab Notebooks.
- Zenodo (CERN) is a free, open access, general purpose research repository for data, documents, and software. Deposits are assigned a DOI (see steps to upload). Groups and projects can create a community space.
Tips for designing research protocols
- How to make your protocol more reproducible, discoverable, and user-friendly (protocols.io)
- How to write an easily reproducible research protocol (American Journal Experts)
Finding published methods and protocols
Clinical trials
- ClinicalTrials.gov - registry run by the National Library of Medicine (NIH)
- International Clinical Trials Registry Platform (ICTRP) - WHO (World Health Organization)'s portal for searching for registered clinical trials
- International registries in the WHO network
Research protocols
Free and UCSF-subscribed methods & protocol resources are listed below. See how to get access to subscription resources through the UCSF Library.
Many of these resources are indexed in PubMed and other research databases. To identify methods articles in PubMed, add the “methods” subheading to a topical search, e.g., gene editing/methods. Tip: Search via pubmed.ucsf.edu and look for Get it at UC for access to subscribed resources.
- Bio-protocol – an open access, peer-reviewed life sciences protocol journal founded by Stanford researchers. Includes protocol preprints and Bio-protocol Exchange for finding and requesting protocols.
- Cold Spring Harbor Protocols (subscription) – an interdisciplinary, peer-reviewed biomedical research techniques journal (invited protocols only)
- Current Protocols (Wiley) (subscription) – over 25,000 curated and edited step-by-step procedures, techniques, and practical overviews in over a dozen topical areas (invited and submitted proposals)
- JMIR Research Protocols – an open access, peer-reviewed journal of research ideas, grant proposals, and study and trial protocols of health-related research and technology innovations
- JoVE (Journal of Visualized Experiments) (subscription) – peer-reviewed, experimental techniques published as videos with accompanying text
- Methods in Enzymology (subscription) – long-running, peer-reviewed publication of research methods in biochemistry and biotechnology
- protocols.io - an open repository with thousands of publicly shared protocols with interactive features, as well as a platform for running and customizing protocols.
- SAGE Research Methods (subscription) - more than 1000 online books, reference works, journal articles, and instructional videos by academics from across the social sciences, including qualitative methods books
- Science of Synthesis (subscription) – critical review of the synthetic methodology developed from the early 1800s to date for the entire field of organic and organometallic chemistry
- Springer Nature Experiments (subscription) – over 75,000 life sciences protocols and methods from Nature Methods, Nature Protocols, Springer Protocols, and Nature Reviews Methods Primers