The journal strongly encourages authors to make all data associated with their submission openly available, according to the FAIR principles (Findable, Accessible, Interoperable, Reusable). Provision of data should, ideally, include data required for reproducing Figures as a stand-alone product.
All data should be curated in a format that allows easy understanding and analysis of the data (e.g. sensible column headers, descriptions in a readme text file). This help will ensure its reuse potential.
Repositories should be selected based on their suitability for the subject area/data being deposited and must provide persistent identifiers for the data (e.g. DOI).
Data should be cited and referenced within the manuscript and should be linked to from a Data Accessibility Statement, which must describe how the data underlying the findings of the article can be accessed and reused. If data is not being made available with the journal publication (e.g. legal constraints), a statement from the author should be provided to explain why. Data obtained from other sources must be appropriately credited.
Data deposited in a repository has many advantages over data files being hosted by the journal. Although the journal will host supplementary data files when absolutely necessary, the journal strongly recommends that data is deposited in a suitable open data repository.
When depositing data for a submission, the below should be considered:
There are many subject-specific or generic repositories now available. If you do not know of a suitable data repositories then the lists are available at https://repositoryfinder.datacite.org/ and http://oad.simmons.edu/oadwiki/Data_repositories.
As the traditional Materials and Methods section often includes insufficient detail for readers to wholly assess the research process, the journal encourages authors to publish detailed descriptions of their methods in open, online platforms such as protocols.io. By providing a step-by-step description of the methods used in the study, the chance of reproducibility and usability increases, whilst also allowing authors to build on the work via versioning or making derivatives of them. This allows the methods to evolve over time but retains a static version that is attached to published research output. Submissions can include images and videos and include the functionality to converse with other researchers who may wish to comment on the methods provided. Protocols.io also allows the complete, step-by-step methodology to be cited, providing researchers with an easy route to finding the information they need whilst crediting the author each time it is used. We believe that publishing such structured methods increases the value, impact and transparency of the research, as well as contributing to Open Science as a whole.
Although the term protocol is more commonly used in clinical research the benefits that protocols.io provides is equally applicable to any structured methods section, across all disciplines.
Publication of the methods in protocols.io releases the information under a CC-BY licence. The choice of whether to make the methods public prior to publication is entirely up to the author (see below). It is also completely free to use.
The protocol/methods site can very easily be setup and incorporated into a manuscript that is being prepared for submission. To publish your methods on protocols.io, simply:
Editors and reviewers will be able to see your protocol with this DOI, but it will not be publicly visible unless you opt to make it open. If your article is published, this referenced link will automatically make your protocol publicly available, enabling readers to view your detailed methods.
For a quick introduction video to protocols.io, visit https://www.protocols.io/welcome?video.
If research includes code, statistical analyses, or algorithms, we recommend that authors upload a working instance of their code and data to Code Ocean. Code Ocean is an online computational reproducibility platform that provides researchers with an easy way to share, validate, and discover code published in academic journals. Code Ocean will mint a DOI for the submitted code, thereby allowing for attribution and citation tracking.
The platform provides free and open access for users to view and download published code, data, metadata, and computational environments. Upon registration, readers can execute all published code online, without needing to install anything, making the reproduction of results simple and painless.
Upload your code to Code Ocean using the following steps: