- FORCE11 has developed a useful overview for reporting in the life sciences. Please review these recommendations before submitting. Recommendations cover the following areas: Sequence Molecule Identification, Reporting of Antibodies, Reporting of Model Organisms, Reporting of Cell Lines, Constructs, and Reporting of Knockdown Reagents.
- Large domain-specific datasets should be deposited in a public repository (e.g. GenBank, INSDC, Protein Data Bank, UK Stem Cell Bank, Addgene, RIKEN Bioresource Centre) and an accession number or access address provided in the published article. Additional databases may be found by consulting the BioSharing database, re3data.org, or the NIH Data Sharing Repositories list.
- Where suitable domain-specific repositories do not exist, authors may deposit in either Dryad, Dataverse, the Open Science Framework, or an institutional repository and provide the access information with the manuscript. Alternately, authors may choose to deposit non-standard data (including figures, posters, rich media) on Figshare or PeerJ Preprints, for example. In all cases, the DOI reference (where applicable) should be provided in the article.
- Any supporting data sets for which there are no suitable repositories may be made available as publishable Supplemental Information files by PeerJ.
- Data should be provided in an appropriate, machine-readable format. Note: formats such as PDF, Powerpoint, and images of tables etc. are not considered suitable for raw data sharing.
- Where appropriate, physical materials (for example mutant seed stock, or paleontological specimens), should be deposited in recognized centers (for example seed stock centers for the former, or recognized museums or institutions for the latter).
- A non exhaustive list of repositories for physical materials such as cell lines or mutant strains includes the RIKEN Bioresource Centre; the Jackson Laboratory; the European Mouse Mutant Archive; the European Conditional Mouse Mutagenesis Program; the American Type Culture Collection; the Knockout Mouse Project; Addgene; the Mutant Mouse Regional Resource Centers.
- Where novel research compounds are used, their chemical identity must be disclosed.
- Publications using commercial antibodies should report the supplying company and code number for all antibodies used. We recommend reporting using the following format:
- In accordance with the principles in Sharing Publication-Related Data and Materials (National Academies Press, 2003), research using proprietary data must also evaluate a piece of comparable public data if the authors cannot or do not make the proprietary data available.
- For software papers, 'materials' are taken to mean the source code and/or relevant software components required to run the software and reproduce the reported results. The software should be open source, made available under an appropriate license, and deposited in an appropriate archive. Data used to validate a software tool is subject to the same sharing requirements as any data in PeerJ publications.
PeerJ will 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 focussed. 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 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.
Articles which report on clinical trials must follow the WHO definition of a clinical trial.
In accordance with the ICMJE guidelines, all trials initiated from July 1st, 2005 must be registered in an approved registry. Unregistered 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.
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 (not only with page references, but also with sufficient text excerpted from the manuscript to explain how all applicable items were accomplished).
PeerJ requires the prospective registration of systematic reviews (for example, in a registry such as PROSPERO). Authors should provide the registry number 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.
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 the description of new bacterial species should address a biological question or hypothesis as the focus of the submission.
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. Please note that PeerJ will be archived in PubMed Central 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 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, 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, 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.
These policies are made available under the Creative Commons CC BY 4.0 license and can be copied for reuse with attribution.