Publishing Ethics
Bio-protocol fully supports the Committee on Publication Ethics (COPE) guidelines, and follows their flowcharts for dealing with potential breaches of publication ethics. Bio-protocol also follows, as far as possible, guidelines established by the Council of Science Editors (CSE) and the International Committee of Medical Journal Editors (ICMJE). These include but are not limited to: standards for treatment of research subjects; falsification and fabrication of data; guidelines for authorship; and piracy and plagiarism.
Appealing an Editorial Decision
Authors can appeal an editorial decision by emailing the Executive Editor that handled their submission with "Appeal of Editorial Decision" in the subject line of the email. The Executive Editor will guide the author on how to prepare a detailed appeal letter, which should state precisely why the author is appealing a decision. Authors might be required to submit relevant supporting materials such as extra material, additional factual input or revisions.

At Bio-protocol, the formal appeal letter will be discussed by at least 5 members of the editorial board. The Executive Editor will mediate all exchanges between authors, editors and peer reviewers. We aim to make a decision within three weeks of receiving the formal appeal letter. The editor’s decision following an appeal is final.
Authorship and Contributorship
Authorship: Bio-protocol supports and adheres to the ICMJE guidelines regarding authorship, authorship criteria, and the scope and responsibilities of corresponding authors. All authors are expected to take responsibility for the content contained within their manuscripts submitted to Bio-protocol. All manuscript authors are contacted via email at the time of submission to ensure that they are aware of and approve the submission, as well as its content and acknowledgment of other listed authors.

Contributorship: Bio-protocol follows the ICMJE guidelines regarding contributorship. Examples of activities such as acquisition of funding, or writing assistance, or providing published data or materials alone do not satisfy the authorship criteria. Those whose contributions do not justify authorship may be listed individually or together as a group in the acknowledgments section. Authors should obtain written permission to mention any individuals listed in the acknowledgments.

Submission of Previously Published Work: Bio-protocol publishes protocols, methodologies, and research techniques that have previously been used to produce data that are already published in the results-oriented peer-reviewed research literature. One primary method for Bio-protocol to publish this content is to invite contributions from authors that have published methods in brief that are used in the results-oriented literature but not described in sufficient detail for others to replicate. Bio-protocol invites authors to publish a full and detailed version of their experimental protocols and workflows.

Bio-protocol requires that the submitted manuscript does not significantly overlap with any other article published previously in a scientific journal. If an author uses representative results or figures from a previous publication, they are required to get permission from the original publisher and then cite this use appropriately. Additional details can be found in the Plagiarism section below.

Bio-protocol also requires authors to acknowledge previously published work (where the protocol is derived from) in both the acknowledgments and references.

Editors and Reviewers as Authors: Editors or reviewers must recuse themselves from the review process and editorial decision about their own work. Additional details can be found at Competing Interests.
Commercial Considerations and Editorial Independence
While building our business model to support the free publication of peer-reviewed protocols, we have always focused on ensuring that Bio-protocol content is shielded from any editorial pressure that may come from advertisements. Although we are confident that the advertising business has no effect on the selection of protocols in Bio-protocol, we recognize that it is critical to acknowledge any possible bias in conflict of interest statements, and to continue to protect editorial integrity and independence. The following are the steps we have already taken to shield Bio-protocol journal content from the advertising business.

First, our initial level of protection is provided by the independence of our Editorial Board from the business side. Our editors are selected and/or vetted by the Editor-in-Chief solely based on their academic achievements and their research expertise in a field relevant to the scope of Bio-protocol. The Editor-In-Chief does not participate in the development of the business side of Bio-protocol, and he serves on the Bio-protocol Advertising Integrity Board to ensure all advertisements and commercially sponsored publications do not undermine the reputation and credibility of editorial content, and do not influence editorial decisions.

Submission to Bio-protocol occurs by invitation, self-submission, or in response to recommendations by editors from our collaborating journals. The primary approach for submission is via invitation by Bio-protocol associate editors. While reading the scientific literature for their own research projects, our associate editors check whether the research publication includes a protocol that could be of broad utility to researchers in their community. After determining the procedure has not already been published as a detailed protocol in any other scientific journal (unless there are significant modifications to the published protocol), our associate editors recommend the protocol and enter the names of the authors of the primary research article in our editorial management system. Invitations are then sent to the authors by the executive editor on the behalf of associate editors through the system, without interference from the executive editor.

The second approach for submission is via collaboration with our partner journals. Submission to Bio-protocol is not a requirement for publication in the partner journals, and the editors at our partner journals do not select specific protocols to be published by Bio-protocol. The following is how our partner journals work with us.

  • In their instructions to authors, they mention the partnership and encourage their authors to submit detailed protocols to Bio-protocol.
  • In their revision and acceptance letters, the editors encourage authors to submit specific protocols (when appropriate) to Bio-protocol and give them the link to Bio-protocol (https://bio-protocol.org/login.aspx?in=1). These submissions will then be reviewed by our editors to make sure they satisfy the same criteria used in the primary approach described above.
  • They create a link from their research articles to the protocols in Bio-protocol that are derived from it.
  • We highlight the partnership in our invitations to their authors.

Self-submission is via our online presubmission system (https://bio-protocol.org/Presubmission.aspx). The submitted presubmission inquiries are reviewed by our associate editors using the same criteria described above.

In each case, the selection of protocols is made by our associate editors and is based solely on the scientific merit of the protocol and the credibility of the published research, ensuring that the selection of protocols in Bio-protocol is not influenced by the development of business projects at Bio-protocol.
Competing Interests
The full policy for competing interests is available online.
Corrections, Retractions, and Editorial Expressions of Concern
Authors are requested to notify the Executive Editor that handled their submission about any errors identified in their published protocol as soon as possible after they become aware of the error. The errors will be corrected and the protocol will be updated clearly indicating that it is a correction published in a later issue. A significant error can also lead to retraction of a protocol.

Bio-protocol allows authors to have their names or/and affiliation changed after publication as long as the request is reasonable, and the request includes the written permission of both the corresponding author and the person whose name or affiliation is changed. If any changes are made, a correction alongside the article will be published online to maintain a transparent and reliable record of the published work. All authors will be informed about any changes made.

Protocols may be retracted by authors or editors due to falsification, irreproducible data, or other gross errors. A retraction notice will appear in a later issue including the title of the original article with an explanation of why it was retracted.

Editors may consider issuing an expression of editorial concern if they have well-founded concerns regarding content (as follows) that would potentially mislead readers and result in the irreproducibility of the protocol.

  • When multiple users (3 or more) from different research groups reported that they failed to reproduce the protocol, we have established a mechanism for revising/improving the description of the protocol to make it easier to reproduce. Our editorial office will contact the authors to trouble shoot to see what the problem is. Some protocols are technically difficult, and so people might not be able to get them to work through no fault of the authors. In that case, we’d request the authors to publish an updated version (or a correction version) of the protocol highlighting technically difficult steps (and perhaps supplement those steps with video instruction). If that mechanism does not sufficiently improve the reproducibility of the protocol (e.g. a previous user or a new user is still unable to reproduce the modified protocol), we will issue an expression of concern to indicate that multiple users have had trouble reproducing it.
  • The editors of the related research article published a statement of concern.

As an expression of concern carries the same risks to a researcher's reputation as a retraction, expressions of concern should only be issued when other avenues of investigation have been completed, are inconclusive, but there remain strong indicators that the concerns are valid.
Plagiarism
Plagiarism consists of two forms: a) self-plagiarism, in which authors reuse significant parts of their own previously published work without appropriate attribution; and b) copying, in which authors present someone else's published work as their own. Significant plagiarism will be determined by the Associate Editor assigned to the manuscript, and if found to violate the acceptable standard of using other pieces of work without appropriate attribution or permission to republish, will not be accepted for publication at Bio-protocol. If significant plagiarism is found after publication, the protocol will be considered for retraction. Minor incidents of plagiarism without intent, for example using several lines from their own previous Materials and Methods section of a paper, will not be considered a violation of plagiarism ethics.
Sharing of Resources
We expect our authors to share materials from their protocols upon request. Relevant materials include strains and isolates, vectors, gene constructs, seeds, cuttings, genotypes, ecotypes, tissue samples, and other similar materials. Authors must also submit data and materials from their protocol to appropriate public repositories wherever applicable.
Research Ethics
Animal and/or Human Subjects: We expect that research involving animal and/or human subjects is to be conducted to the highest ethical standards. For animal research, we recommend following the guidelines established by Animal Research: Reporting of In Vivo Experiments (ARRIVE). For protocols that include the use of live animals (e.g., vertebrates and higher invertebrates), the authors must mention the specific ethics committee(s) that reviewed the experiments and confirm that all of the experiments were performed in accordance and compliance with the established guidelines. All manuscripts and videos must include a statement that the demonstrated protocol was approved by the authors' animal use governing body (the statement should be included in the video legend). All protocols that have used human 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 (or provide a detailed explanation for why consent was not obtained). Authors should also ensure that they have the proper permission from their institutional review board or other regulatory groups overseeing their studies to film human subjects. Authors must make sure that subjects understand the format and distribution of the publication.
Informed Consent for Publication
We uphold the right to anonymity and take all necessary steps to protect the privacy of those who participate in research or experiments.

Authors must avoid providing identifying information unless strictly necessary for the submission. If identifying information is necessary, authors must confirm that the individual has provided written consent for the use of that information. Consent forms do not need to be submitted with the manuscript, but authors should provide necessary details upon request by editors.

If identifying information is discovered after publication, the article will be temporarily withdrawn while any content compromising participant privacy is removed.
Registering Clinical Trials
Prospective registration in suitable recommended registries (e.g. ClinicalTrials.gov) is a requirement for publication of a protocol related to such trials. Clinical trial registration numbers should be included in the manuscript.
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