Authors must follow the provided template for manuscript preparation and ensure that all information they choose to include is relevant to the protocol described. Bio-protocol requires authors to submit all text and figures as a single Microsoft Word file, while videos must be submitted as separate files. The manuscript should contain the elements described below in the "Protocol format" section below. Abbreviations should only be used if necessary and defined upon first use in the Abstract and again in the main text. Click here to see an example of an article in the standard Bio-protocol format.

Protocol Format

Submitting authors must follow the standard Bio-protocol format, described below. For more details about each element, please see the manuscript template.

1. 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 to them. Keep in mind that your protocol could be useful for researchers from a completely different field; as such, the title should be clear to a broad range of scientists.

2. Author information

Please provide complete affiliation information (department, research institution, city, country) for each author.

3. Abstract

The Abstract should briefly introduce the research field and provide a summary of the protocol, highlighting its goal and advantages over other methods.

4. Key features

Key features are bullet points that convey important elements of the protocol. These 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.

5. Keywords

Include technical or method-related keywords to help readers easily find your protocol using Google or other search engines. Repeat the relevant keywords used in your original research paper (if applicable).

6. Graphical overview

The graphical overview could be a flowchart of the method/procedures or a graphical highlight of key steps; it should not be a simple copy of other images in the manuscript. See an example here. Please provide the graphical overview in a figure format. This section is highly recommended but not mandatory.

7. 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 existing technology of the research field, discuss previously used related methodologies and/or bioinformatics pipelines, and summarize the advantages, limitations, and applications of your approach.

This section should provide a detailed list of all biological materials, reagents, solutions (with recipes), and laboratory supplies required for the successful execution of the protocol, including manufacturer information, catalog numbers, instructions on how to acquire/produce items that are not commercially available, and storage conditions/shelf-life for critical reagents. Be precise about the ingredients used, as a lack of clarity on minor details may lead to the failure of the experiment. Authors should indicate whether any materials are subject to Material Transfer Agreements (MTAs) or if any data are subject to Data Use Agreements (DUAs).

List the equipment used in the experiments, including specific catalog/model numbers.

10. Software and datasets

List individual software or datasets required to complete the protocol, including version, release date, and license. If possible, provide free alternatives to commercial software.

11. Procedure

Provide a step-by-step guide for the use of the software/bioinformatics pipeline. Be specific in your instructions. Provide README files and a DOI for GitHub/Bitbucket repositories if included in the protocol. For wet-lab steps, if such steps are included in the protocol, provide 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."

Make sure to include notes (see General Notes and Troubleshooting below), especially if it would increase the likelihood of successfully running the code and, if applicable, reproducing wet-lab steps. As needed, include images and videos to clarify key steps. Describe the input format for the data, as well as the expected output, such as graphs, lists, etc. Include representative data to illustrate the type of results obtained.

For formatting details for text, figures, tables, and videos, see the manuscript template.

12. Result interpretation

Provide a detailed interpretation of the data obtained above.

13. Validation of protocol

This section aims to reassure readers that the protocol has been tested and can produce reliable results. You may provide evidence that the protocol is robust and reproducible by:

• Providing data directly in this section. Provide validation directly in this section of your submission. Alternatively, if sufficient validation information is already provided in the “Result interpretation” section above, briefly reference it here. For protocols that include wet-lab steps, include information about the number of replicates and controls used.
• Referencing specific data published elsewhere. Cite figures, tables, text, or supplementary materials from the research article or preprint where your protocol was used (e.g., your original work).

Note: We highly encourage authors to provide validation data directly in this section while also citing data published elsewhere, particularly if the original research work is not open access.

14. 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 datasets, experimental systems, or variability.

If stating common problems that might occur, please describe ways to address them.

15. Supplementary information

Include source or extended data and any relevant supporting materials in this section.

16. Acknowledgments

Specify the individual contributions of each author of the manuscript; you may use the example provided in our manuscript template or any other format you deem appropriate. Additionally, 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.

17. 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 reagents/equipment or other advertisers. For more information, see our guidelines for disclaiming competing interests here.

18. 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. For animal research, we recommend following the guidelines established in Animal Research: Reporting of In Vivo Experiments (ARRIVE). For more information, see our publishing ethics notes.

19. 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.