PeerJ is committed to improving scholarly communications and as part of this commitment, authors must make materials, code, data, and associated protocols available at the time of submission for peer review and publication. The preferred way to meet this requirement is to publicly deposit as noted below. Cases of non-compliance will be investigated by PeerJ which reserves the right to act on the results of the investigation.
We strongly recommend (and in some cases require) that authors adhere to the reporting standards which have been adopted by their field (or which apply to their study design).
All statistical results should be reported in full, including the test that was performed, the reason for choosing that test, the corresponding test statistic, sample size, degrees of freedom, the exact p-value expressed up to 2 decimal spaces unless 'p<0.001' or confidence interval, and effect sizes. Where multiple testing is performed, suitable corrections must be made.
Do not report inferential statistics such as p values or confidence intervals for known quantities such as baseline measurements. The spread of the data can be indicated by descriptive statistics such as standard deviation, or quantiles and ranges.
Where appropriate, we recommend that you overlay bar graphs with scatter plots showing individual data points, or use another method to show the distribution of the data, such as boxplots, violin plots, etc.
PeerJ journals consider timely and well-targeted literature reviews of fields with broad cross-disciplinary interest within the journal's scope. While we do not impose a hard limit, we recommend a maximum of 8,000-12,000 words in order to keep the review focused. The review should include a rationale for why it is needed, describe who it is intended for, and include a description of the procedures used to ensure that it is comprehensive and unbiased (for example, the search strategies that were employed). Gaps in the literature, future avenues of research and opportunities for cross-disciplinary collaborations should be clearly identified.
Since, by their nature, literature reviews rely heavily on the published work of others, it is especially important to avoid inadvertent plagiarism by copying and pasting sections of text from the original source. In addition, it is very important, when quoting or paraphrasing, to correctly acknowledge your sources.
We recommend that your review is structured following the guidelines for Literature Review Articles in standard sections.
PeerJ will consider scoping reviews (as literature review submissions) that meet the definition elaborated in Munn et al. (2018).
In accordance with that definition, a literature review should not be used to "...answer a clinically meaningful question or provide evidence to inform practice." If your review does this then PeerJ policy is that it must be submitted as a systematic review/meta-analysis article.
Reference: Munn Z, Peters MDJ, Stern C, Tufanaru C, McArthur A, Aromataris E. 2018. Systematic review or scoping review? Guidance for authors when choosing between a systematic or scoping review approach. BMC Medical Research Methodology 18:143 DOI: 10.1186/s12874-018-0611-x.
PeerJ welcomes articles describing bioinformatics software tools. These articles should present new software tools (or significant new functionality in existing software) of particular interest to the bioinformatics and/or computational biology communities. The described tools should provide new computational or analytical functionality for researchers.
The functionality of the software should, where appropriate, be validated using real-world biological data and/or compared to existing tools. If available as a package (e.g. Python, R, Matlab, Octave), it should be accompanied by a minimal script that downloads the data (if not included in the package), loads it, and performs the analysis to reproduce the results (tables, plots, visualizations etc.) in the manuscript. Documentation & comments must be clear and sufficient to allow a typical user to perform the analysis described in the article. Ideally, the tools should be usable in a workflow that encourages reproducible research practices.
The software must be released under an open source license (e.g. MIT, GPL) and be widely available (i.e. hosted in a public repository such as Github or Bitbucket, or an institutional repository). Use of a version control system (e.g. Git, Subversion etc.) is strongly encouraged, as is adherence to language-specific packaging practices where appropriate. We also recommend the inclusion of appropriate unit tests. The software must be free to noncommercial users, and must be accessible without requiring any personally identifiable information. Software and validation data sets must comply with PeerJ Data and Materials Sharing policies. Reliance on a proprietary software such as Matlab does not preclude the publication but in general, a fully open source method is to be preferred.
Bioinformatics studies that are based on the analysis of previously published datasets (for instance, sequences from TCGA, microarray experiments from GEO, data from TARGET, SEER, NHIRD, NHANES, etc.) must both (i) answer a biological question not considered in the original publication (if there is one) or reassess the data to arrive at a different conclusion and (ii) validate the findings using an independent dataset or using previously unreported clinical or experimental data.
If the submission searches or extracts information from a public database but does not either compare independent datasets or validate the findings using primary data, then this will be considered out of scope (as it is an initial exploration rather than a full research article). Splitting a dataset to form a training and testing set, or pooling multiple datasets without a completely independent validation set will not be considered (see e.g. https://doi.org/10.1073/pnas.102102699).
Articles which report on clinical trials must follow the WHO definition of a clinical trial.
In accordance with the ICMJE guidelines, all clinical trials initiated from July 1st 2005 must be registered in an approved registry listed by the WHO or the ICMJE. Unregistered or retrospectively registered trials will not be considered. Where participant recruitment began before trials were publicly registered, authors must a) register all related clinical trials and include the relevant information, in the Methods section, and b) explain the reason for failing to register before participant recruitment, in the Methods section. Registration must be completed before trial interventions or data analysis are begun.
Specifically, authors must provide a copy of the trial protocol and a completed CONSORT (or TREND) checklist as supplemental information (these documents will also be published with the manuscript, if accepted). The CONSORT flow diagram must also be included, preferably as Figure 1 of the manuscript. The manner of the informed consent should be discussed in the article, and if consent was written, an empty copy of the patient consent form should be provided as a Confidential Supplemental Information file.
Reports of systematic reviews and meta-analyses must include a PRISMA flow diagram as Figure 1, and a completed PRISMA checklist as a Supplemental File (including both page references and sufficient text excerpted from the manuscript to explain how all applicable items were accomplished).
PeerJ requires the prospective registration of systematic reviews that deal with a health-related outcome or report on animal studies. Suitable registries include PROSPERO, which accepts registration of "any ongoing systematic review of studies in humans or animals that has a health related outcome relevant to human health in the broadest sense" and CAMARADES which accepts registration of systematic reviews that report on experimental animal studies. Retrospectively registered reviews will not be considered.
Authors should provide the registry name and number/URL in the abstract. Registry details and protocols will be made available to Academic Editors and reviewers, and published with the final version of the paper.
Authors should identify (within their Methods section) the authors who performed the search strategy. Please describe how disagreements were resolved and identify the referee in the manuscript.
Systematic reviews or meta-analyses should include those terms in the Title, Abstract and / or full manuscript.
Authors should provide the following information in a Supplemental File: 1. The rationale for conducting the meta-analysis; 2. The contribution that the meta-analysis makes to knowledge in light of previously published related reports, including other meta-analyses and systematic reviews.
For meta-analyses on topics that include genetics, authors should provide a completed checklist (as a Supplemental File) outlining information about the study. Download genetics checklist (.doc).
Manuscripts that report on population genetics should include special justification for presenting data based on both limited genetic data (<10 microsatellites or a single, low variability mtDNA region) and/or small sample sizes (<100 individuals). PeerJ does not publish primer notes. Manuscripts that report the characterization of specific primers (such as microsatellites) should include substantial biological analyses, and address a biological question or hypothesis as the focus of the submission.
Manuscripts that report range extensions, life history information, or the description of new species or other taxa should address a biological question or hypothesis as the focus of the submission. Unless there are compelling mitigating circumstances, descriptions of new extant taxa should be based on the whole organism (rather than shells/fragments/organs alone) and be supported by multiple lines of evidence (e.g. morphology, genetics, etc.).
Submissions that screen molecules based on network pharmacology and/or molecular docking calculations must validate the candidate molecules either experimentally, or through molecular dynamics simulations. If the molecular dynamics route is selected, then duplicated simulations (at least 50 ns each) should be conducted on the best ligands.
In order to increase discoverability, when naming a new species we recommend that the names are mentioned in the title (where feasible) and in the abstract of your article. If multiple new species are being named then it may not be practical to include all or any of them in the title due to space constraints.New Zoological Taxonomic Names: Electronic publication of new zoological taxonomic names is now permitted by the ICZN with an amendment to the current Code. To name a new zoological species, genus or family, authors must comply with rules of the ICZN that require details of the publication to be entered into the official ICZN registry, Zoobank. PeerJ is listed in PubMed Central SCIE and CLOCKSS, and will show up as a known journal during the ZooBank registration process.
- In the metadata, the globally unique identifier (GUID), currently a Life Science Identifier (LSID), should be listed with the new species name. For example:
Brachycephalus mariaeterezae sp. nov. urn:lsid:zoobank.org:act:74D8D85E-BE68-4A51-AF85-DC97C564D458
- Authors must use the following text in the Methods section:
"The electronic version of this article in Portable Document Format (PDF) will represent a published work according to the International Commission on Zoological Nomenclature (ICZN), and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. This published work and the nomenclatural acts it contains have been registered in ZooBank, the online registration system for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix http://zoobank.org/. The LSID for this publication is: [INSERT HERE]. The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central SCIE and CLOCKSS."
- The globally unique identifier, currently a Life Science Identifier (LSID), should be listed under the new taxon name in the Results Section.
-Assuming an LSID is obtained, authors will be made aware of them by PeerJ staff and must use the following text in the Methods section:
"The electronic version of this article in Portable Document Format (PDF) will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants (ICN), and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. In addition, new names contained in this work which have been issued with identifiers by IPNI will eventually be made available to the Global Names Index. The IPNI LSIDs can be resolved and the associated information viewed through any standard web browser by appending the LSID contained in this publication to the prefix "http://ipni.org/". The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central SCIE, and CLOCKSS".
- An additional ICN publication requirement effective January 1, 2013: all manuscripts naming fungi must obtain the citation of an identifier issued by a recognized repository such as MycoBank or Index Fungorum and include it in the protologue (everything associated with a name at its valid publication). Life Science Identifiers (LSIDs) or Globally Unique Identifier are only required for fungi.
- In the Methods section, authors must include a sub-section called "Nomenclature" using the following wording (this example is for taxon names submitted to MycoBank; please substitute appropriately if the name was submitted to Index Fungorum):
"The electronic version of this article in Portable Document Format (PDF) will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants, and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. In addition, new names contained in this work have been submitted to MycoBank from where they will be made available to the Global Names Index. The unique MycoBank number can be resolved and the associated information viewed through any standard web browser by appending the MycoBank number contained in this publication to the prefix "http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=". The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central SCIE, and CLOCKSS."
- Authors of new names and new combinations must provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). Upload these certificates as Supplemental Files at submission.
- As required by the Bacteriological Code, the IJSEM publishes Validation Lists containing new names that were effectively published in any journal other than the IJSB/IJSEM. To complete validation of new names effectively published, authors should submit a covering letter and three reprints or photocopies or a PDF file of the published article(s) to the IJSEM Editorial Office.
- All new viral taxa must be approved by ICTV before any individual taxon (and its name) can be official. To create a new taxon, a proposal should be submitted to the ICTV using the procedures detailed in their FAQ.
This proposed new species [INSERT NAME] has been submitted to the ICTV for consideration. This name is only valid and official after the ICTV has approved the name, and it has been ratified by the membership: [INSERT URL].
This proposed new species [INSERT NAME] has been approved by the ICTV. This name is only valid and official after the ICTV has both approved the name and it has been ratified by the membership: [INSERT URL].
This proposed new species [INSERT NAME] has been approved and ratified by the ICTV. It has not yet been published in the annual taxonomy: [INSERT URL].
This new species [INSERT NAME] has been approved and ratified by the ICTV as reported in: “Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)”. Arch Virol. 2018 May 12. doi: 10.1007/s00705-018-3847-1. PubMed PMID: 29754305.
These policies are made available under the Creative Commons CC BY 4.0 license and can be copied for reuse with attribution.