Protocol Preparation Guidelines for Authors
Bio-protocol publishes protocols that have not been previously described in sufficient detail in the Methods sections of original research articles or in other types of publications (
e.g., book chapters). Condensed methods currently published by most journals can be hard to reproduce.
Bio-protocol helps to fill this gap by providing a platform for clearly written peer-reviewed protocols that contain sufficient detail to ensure their reproducibility. The goal of our published protocols is to provide enough information for a novice to perform an experiment successfully with only limited advice or supervision. Any protocol, whether novel or basic, that has not yet been described in detail in the published literature is a good candidate for publication in
Bio-protocol.
Authors should submit their manuscript via the Bio-protocol website
here. Please see the general guidelines below that describe the main components of protocols published in Bio-protocol. We request that authors follow the
Bio-protocol Manuscript Template for manuscript preparation. For questions, contact the editorial team, at
editorial@ed.bio-protocol.org. If your protocol does not fit our standard template, or if you have suggestions to improve our template and author guidelines, contact our Managing Editor, Marisa Rosa (marisa.rosa@ed.bio-protocol.org).
General Guidelines
Bio-protocol encourages authors to submit manuscript text and figures as a single Microsoft Word file. Authors must follow the provided
template for manuscript preparation. We have no limits on word count or the number of figures/videos. Figures and tables should be embedded in the Word file, while videos must be submitted as separate files. The manuscript should contain the elements described below in the "Protocol format" section. Abbreviations should only be used if necessary and defined upon first use in the Abstract and in the main text. Click
here to see an example of an article in the standard
Bio-protocol format.
The Bio-protocol Manuscript Template can be downloaded
here.
Submitting authors must follow the standard
Bio-protocol format. Protocols published in
Bio-protocol consist of the following sections. For more details about each element, please see the
Manuscript Template:
- Protocol Title
The Title should indicate the goal of the protocol and provide enough detail to help a prospective researcher determine whether the protocol is of interest. Keep in mind that your protocol could be useful for researchers from a completely different field. When using specific terminology, make sure that the title can be understood by a broad range of scientists.
- Author Information
Please provide complete affiliation information (department, research institution, city, country) for each author.
- Abstract
The Abstract should provide a brief summary of the protocol and highlight the goal and advantages of the protocol. It should also contain one or two sentences describing the context in which this assay/method was developed.
- Key Features
Key Features are bullet points that convey important elements of the protocol. Key Features should not simply repeat or condense ideas conveyed in the Abstract. Instead, they should highlight characteristics that will allow readers to determine whether the protocol is relevant to their work. See our protocol template for examples.
- Graphical Overview
Provide the graphical overview in figure format. This component is highly recommended, but not required. The overview could be a flowchart of the method/procedures or highlights of the key steps. See an example here.
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Keywords
Include technical or method-related keywords to help readers easily find your protocol using Google or other search engines, and repeat the relevant keywords used in your original research paper (if applicable).
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Background
Briefly introduce the research area(s) that your protocol can be used to advance, providing the rationale for developing the protocol. Place the protocol in the context of the existing technology of the research field, discussing previously used related methodologies, and summarizing the advantages, limitations, and applications of your approach.
- Materials and Reagents
Imagine that the reader of the protocol is a novice. This section should provide a detailed list of biological materials, reagents, and solutions (with recipes) required for the successful execution of the protocol, including manufacturer catalog numbers, instructions on how to acquire/produce items that are not commercially available, and storage conditions and shelf-life for critical reagents. Be precise about the ingredients used, as a lack of clarity on minor details might lead to the failure of the experiment. Authors should indicate whether any materials are subject to Material Transfer Agreements (MTAs), or any data are subject to Data Use Agreements (DUAs). Organize the items into four subcategories when it applies: Biological Materials, Reagents, Solutions, and Recipes.
- Laboratory Supplies
List the laboratory supplies used in the experiments, including specific manufacturer catalog numbers and references for items that are not commercially available.
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Equipment
List the equipment used in the experiments, including specific catalog/model numbers.
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Software and Datasets
List individual software or datasets used in the experiments, including version and release date. Provide references for items that are not commercially available.
- Procedure
List all steps of the procedure chronologically, as it makes the protocol easier to follow. Be specific in your instructions. Include details for material and reagents used (e.g., volume added, specific container/tube, and incubation time) and the conditions in which the step is performed (e.g., temperature, agitation speed, and equipment settings); avoid using vague terms such as "several" or "enough."
At crucial steps, make sure to include labels ("Caution," "Pause point," or "Critical," as appropriate) and notes (see General Notes and Troubleshooting below), especially if it would increase the likelihood of successfully repeating the experiment. As needed, include images and videos to clarify key steps and representative data to illustrate the type of results obtained.
For formatting details for text, figure, table, and video, see the Manuscript Template.
- Data Analysis
Provide a detailed description of data processing and analyses, including statistical tests, criteria for data inclusion/exclusion, and details on the recommended number of biological and technical replicates in each experiment. Highlight any specific skills necessary to perform the analyses (e.g., expertise using Linux, R, or other specific data analysis software).
When a detailed description of the data analysis method already appears in a published or posted research article, summarize the analysis method and cite the publication or preprint. Please indicate clearly where the description of the analysis can be found (e.g., Supplemental information or Figure X). If the published description has restricted access, please request permission to "reprint" the analysis method in Bio-protocol.
- Validation of Protocol
Please provide the evidence that this protocol is robust and reproducible. For experimental protocols, include information about the number of replicates and controls that were used to validate the protocol.
Types of Evidence:
- Reference specific data in a research article published or posted by you or others, e.g., specific figures or supplementary materials in the article or preprint.
- Provide data directly in this section of your Bio-protocol submission.
- General Notes and Troubleshooting
Include comments that apply broadly to the protocol and are not fundamental to completing individual steps. For example, address limitations of the protocol, its applicability to other experimental systems or model organisms, or variability.
Troubleshooting states common problems that might occur and describes ways to address them.
- Acknowledgments
Acknowledge funding sources that have supported the work. If the protocol was adapted or modified from previous work, acknowledge the relevant publications as well. If your original research was published in one of our partner journals, cite it here and add its DOI.
- Competing Interests
Provide a statement of financial and non-financial competing interests on behalf of all authors. At Bio-protocol, one typical type of financial competing interest is the receipt of funding or free products from the vendors of the reagents/equipment or other advertisers. Other examples of financial and non-financial competing interests can be found at PLOS.
- Ethical considerations
All protocols that have used human and/or animal subjects must mention the specific ethics committee that approved the described experiment. Protocols including human subjects should also indicate that informed consent was obtained from all subjects. Protocols including clinical trials should clearly state the name of the trial registry and the clinical trial registration number in the manuscript.
- References
Cite journal articles that are accepted, published, or posted as preprints. For in press accepted articles, add the expected date of publication. Add the relevant citations for all datasets, program code, and other resources used in the protocol.
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Supplementary information
Include extended data, supplementary information, or source data in this section.