Methods and Protocols Resources

What is a protocol?

A protocol is a document that describes how a clinical trial or research project is conducted. It is an essential tool for ensuring the validity and reproducibility of research results. Protocols typically include sections such as: objectives, study design, selection and exclusion of subjects, methodology, statistical considerations, ethical guidelines, organization of the experiment, and data handling.

The terms methods and protocols are often used interchangeably, though methods are sometimes considered novel techniques whereas protocols are established methods that have already been used in primary research publications. Protocols can also be for computational workflows, operational procedures, and safety checklists.

Methods and protocols collections

Subscription resources restricted to UCSF users are indicated by (subscription). Many of the resources below are indexed in PubMed and other research databases. 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 (subscription) – thousands of peer-reviewed, step-by-step research procedures in a dozen topical areas, including bioinformatics, pharmacology, and toxicology. See subscribed titles.  
  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. UCSF-subscribed titles are indicated by a blue dot.
  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. protocols.io - an open repository of over 5000 publicly shared protocols with interactive commenting, as well as a platform for running and customizing protocols. UC’s premium account allows unlimited numbers of private 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) – synthetic methodology for organic and organometallic chemistry. Peer-reviewed.
  11. Springer Nature Experiments (subscription) – over 60,000 protocols and methods from across the life sciences. Combines content from Nature Methods, Nature Protocols, and SpringerProtocols.

Resources for designing protocols

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