Advances in scientific discovery are built on the contributions of prior researchers. Having the ability to reproduce research results is a cornerstone for advancement, which is accelerated when researchers have accurate roadmaps. Protocols and methods are a body of literature that describe experimental procedures in detail.

The terms protocols and methods are used interchangeably at times. A distinction is that a research method is 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. Descriptions of experimental procedures are included in publications of original research. While the methods sections of research articles are typically sufficient to provide an expert in the field with enough context to interpret the published results, these sections may not provide enough information for a researcher to replicate an experiment. Someone seeking to do so may need to consult other sources for more detailed descriptions.

Protocols and methods are found as stand-alone publications in a variety of literature types: method-focused journals, book series, and preprint servers. Authors of methods publications can benefit reputationally. The most highly cited publication in Web of Science is a protein methods article, which has been cited over 350,000 times (Lowry et al., 1951). A good protocol can save researcher hours in the lab by starting with proven methodologies for their research.

Open protocol platforms and preprint servers

Support for rapid, transparent and low-barrier sharing of methods literature has contributed to the development of open protocol platforms and preprint servers. Examples include:

• Bio-protocol exchange: founded by Stanford researchers in 2011. Contains ~2,000 preprint protocols and citations to 6 million published protocols. Companion sites include:
• bio-101, features basic methods.
• Bio-protocols Journal (see below).
• Protocols.IO: Open access repository of science methods and collaborative research platform. Registration is free, but required to view content. Recently acquired by SpringerNature.
• Protocol exchange: an open preprint server sponsored by SpringerNature Experiments.

Content on these platforms may represent the final published version or lead to a subsequent publication that appears in an edited journal or book series.

Open methods and protocols journals

Open methods and protocols journals are supported by author publishing charges (APCs) and are listed in the Directory of Open Access Journals (DOAJ).

• Bio-protocols Journal – Part of the Bio-protocols platform (see above). Entries in the journal are indexed in Pubmed and GoogleScholar, and supported by APCs.
• Biology Methods and Protocols (Oxford Press) – open in 2016. Indexed in Pubmed and GoogleScholar.
• JMIR Research Protocols (JMIR) – open in 2012. Indexed in Pubmed and GoogleScholar.
• Methods and Protocols (MDPI) – open in 2018. Indexed in Pubmed and GoogleScholar.
• STAR Protocols (Elsevier/Cell) – open in 2020. Indexed in Pubmed and GoogleScholar. 

There are other methods and protocols journals titles with a hybrid publishing model with some content published openly and other articles behind a paywall. Methods articles are also published in the general scientific literature.

Collections of protocols and methods

Several publishers offer packages of methods literature. These resources allow subscribers to conduct focused searches for bioscience protocols and methods within a collection of methods journals and book series. Examples include:

Cold Spring Harbor Protocols: Cold Spring Harbor Laboratory has a well-respected press that includes manuals and methods books. Noteworthy content in this collection includes and extensive recipes collection and its laboratory organisms series. CSH Protocols are indexed in Google Scholar.

Current Protocols (Wiley): A collection of step-by-step techniques, procedures, and practical overviews. This collection emphasizes curated, highly edited methods rich in detail, practical advice, and troubleshooting. The content is freely searchable, with much of the full text behind a paywall. Indexed in both Pubmed and Google Scholar.

Journal of Visualized Experiments (JoVE): A video journal platform featuring researcher contributions of methods for biological research and publisher-generated educational content. Jove content is indexed in both Pubmed and Google Scholar.

SpringerNature Experiments: A large collection of protocols and methods which combines content from Nature Methods, Nature Protocols, Nature Research, and Springer Protocols. Content is freely searchable, with much of the full-text behind a paywall. The journal-based content is indexed in Pubmed and the entire collection is searchable in Google Scholar.

• Nature Methods contains peer-reviewed cutting-edge, novel methods that address key questions in biology.
• Nature Protocols publishes protocols from basic “classic” protocols to innovative techniques.
• Springer Protocols is the largest collection of published protocols in biomedicine and life sciences featuring content from well-known book series including Methods in Molecular Biology.

Dissertations and theses

Theses and dissertations often have more detailed methods sections than journal articles and include research methods that may not be published elsewhere. Examples of theses collections or discovery platforms include:

• Dissertations and Theses (Proquest) is a subscription service containing theses and dissertations (mostly from North American universities).
• Networked Digital Library of Theses and Dissertations is an international collection that contains over 6 million digital theses.
• University repositories offer open access to institutional theses collections. Examples include OhioLINK; University of Florida; and DSpace@MIT.

Summary

In both Europe (Open Science, 2023) and the United States (FACT SHEET, 2023) government research funding policies aspire to make access to funded research output open and reproducible. This has expanded the output of published research findings to include data, code, and methods to accompany the research article.

Recognizing methods and protocols literature as a distinct publication type in bioscience education can promote the adoption of open science practices.

References

• Lowry, O., Rosebrough, N., Farr, A., & Randall, R. (1951). Protein Measurement with the Folin Phenol Reagent. JOURNAL OF BIOLOGICAL CHEMISTRY, 193(1), 265–275.
• FACT SHEET: Biden-Harris Administration Announces New Actions to Advance Open and Equitable Research | OSTP. (2023, January 11). The White House. 
• Open Science. The EU's open science policy (2023, February 10).

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