Reproducibility

Open Data

The journal strongly encourages authors to make all data associated with their submission openly available, according to the FAIR principles (Findable, Accessible, Interoperable, Reusable). This should be linked to from a Data Accessibility Statement within the submitted paper, which will be made public upon publication. If data is not being made available with the journal publication then ideally a statement from the author should be provided within the submission to explain why. Data obtained from other sources must be appropriately credited. When depositing data for a submission, the below should be considered:

  • - The repository the data is deposited in must be suitable for this subject and have a sustainability model.
  • - The data must be deposited under an open license that permits unrestricted access (e.g. CC0, CC-BY). More restrictive licenses should only be used if a valid reason (e.g. legal) is present.
  • - The deposited data must include a version that is in an open, non-proprietary format.
  • - The deposited data must have been labelled in such a way that a 3rd party can make sense of it (e.g. sensible column headers, descriptions in a readme text file). 
  • - Research involving human subjects, human material, or human data, must have been performed in accordance with the Declaration of Helsinki. Where applicable, the studies must have been approved by an appropriate ethics committee. The identity of the research subject must be anonymised whenever possible. For research involving human subjects, informed consent to participate in the study must be obtained from participants (or their legal guardian). 
  • - A ‘Data Accessibility Statement’ should be added to the submission, prior to the reference list, providing the details of the data accessibility, including the DOI linking to it. If the data is restricted in any way, the reasoning should be given. 

A list of data repositories is available at http://oad.simmons.edu/oadwiki/Data_repositories.

Structured Methods

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:

  1. Register at protocols.io and create your protocol
  2. Select ‘Get DOI’ on the protocols.io menu tab
  3. Include the DOI in the Methods section of your manuscript, for example https://doi.org/10.17504/protocols.io.[protocol number].

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.

Open Code

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:

  1. Sign up/login to Code Ocean
  2. Upload and submit the code and data associated with your article.
  3. Configure your environment, run your code and submit.
  4. Code Ocean will verify the code is operational and help with any issues
  5. Your executable code will be published on Code Ocean. It will be assigned a unique URL you can share, as well as a DOI that can be used to cite it.
  6. Add the DOI that has been provided into your journal submission so that there is a direct link for the editors, reviewers, and readers to access.