Methods and Protocols Resources

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 process or 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, whereas a research protocol is the step-by-step process for producing results using the chosen method. A clinical protocol is is a document that describes how a clinical trial will be conducted and how the safety of the trial subjects and integrity of the data will be protected.

Protocols can also be written for computational workflows, operational procedures, and safety checklists.

Published methods and protocols

The UCSF Library subscribes to the methods & protocol resources listed below. Recommended freely available resources are also included. See how to get access to subscription resources

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.

  1. Bio-protocol – a free, peer-reviewed life sciences protocol journal founded by Stanford scientists
  2. Cold Spring Harbor Protocols (subscription)  an interdisciplinary, peer-reviewed biomedical research techniques journal
  3. Current Protocols (Wiley) (subscription) – over 25,000 curated and edited step-by-step procedures, techniques and practical overviews in over a dozen topical areas.  
  4. 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.
  5. JoVE (Journal of Visualized Experiments) (subscription) – peer-reviewed, experimental techniques published as videos with accompanying text. 
  6. Methods in Enzymology (subscription) – long running peer-reviewed publication of research methods in biochemistry and biotechnology
  7. Protocol Exchange – open and free protocol sharing site with 1000 contributions, many with videos. Managed by Nature Protocols.
  8. - an open repository with thousands of publicly shared protocols with interactive features, as well as a platform for running and customizing protocols. UC’s premium account allows unlimited numbers of private protocols and groups.
  9. SAGE Research Methods (subscription) - more than 1000 online books, reference works, journal articles, and instructional videos by academics from across the social sciences, including a large collection of qualitative methods books. 
  10. 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. 
  11. Springer Nature Experiments (UC subscription) – over 75,000 protocols and methods from across the life sciences. Combines content from Nature Methods, Nature Protocols, SpringerProtocols, and Nature Reviews Primers Methods. Filter results by technique, antibody, organism, and more.

Resources for designing protocols

  1. Clinical Trial Protocol Development from UCSF’s Clinical Research Resource HUB offers several protocol templates and related resources. Cancer Center-specific templates and resources are also available. 
  2. Protocol Registration & Results System or a similar registry is required for publication of clinical trial results in many journals. See definitions of protocol data elements, templates, and tutorials
  3. EQUATOR Network provides reporting guidelines for all study types
  4. How to write an easily reproducible research protocol from American Journal Experts
  5. How to make your protocol more reproducible, discoverable, and user-friendly from
  6. Systematic review evidence synthesis protocol templates and PRISMA checklist resources from Cornell University Library

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