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Sharing Materials, Software and Code
Sharing Materials, Software and Code

SAFE Journal of One Health is committed to ensuring the availability of materials, software, and code that underpin published research, encouraging reuse and facilitating reproducibility.

All authors are expected to make research materials available without restriction upon publication, and to share software and code following open-source standards and best practices.

Related policy: Data Availability

Overview

The journal is committed to ensuring the availability of materials that underpin research. Sharing materials encourages reuse and facilitates reproducibility.

The journal reserves the right to issue a correction, expression of concern, or retraction if undisclosed restrictions on sharing are discovered after publication. The journal will contact authors' institutions and funders as appropriate.

The journal's policy on availability does not require that materials must be made available free of charge.

Sharing Research Materials

All authors submitting to the journal are expected to make all research materials that may reasonably be requested by others available without restriction upon publication of the work. Where proprietary or justified restrictions exist, such as those intended to protect privacy or confidentiality of human research subjects, their disclosure in the Materials and Methods section and a description of the conditions under which the materials may be accessed is expected.

Editors and reviewers should verify the availability of materials during the peer review process and contact the journal if any undisclosed restrictions are discovered.

The journal strongly encourages authors to deposit copies of materials including plasmids, cell lines, and model organisms to established repositories. Using FAIRsharing or the RRID Portal on the Registry of Research Data Repositories (Re3Data) is suggested to find the most appropriate repository.

Although authors are encouraged to deposit materials in relevant repositories, materials may be shared directly upon request. When sharing materials directly, authors are expected to provide them in a timely manner and with any associated materials needed to enable their reuse.

Research Resource Identifiers

The journal encourages authors to use Research Resource Identifiers (RRIDs) to cite and uniquely identify resources used in their research.

The RRID Portal provides a searchable database of existing RRIDs and includes instructions for creating new ones. Authors should include RRIDs in the text of their manuscripts to identify antibodies, plasmids, model organisms, cell lines, and tools. The following are examples:

Accessing Materials

Contact the journal if you encounter difficulties obtaining materials associated with published articles.

The journal cannot arbitrate if any disputes arise, especially with respect to Material Transfer Agreements (MTAs).

Sharing Software

All researchers submitting to the journal in which software is the central part of the manuscript are expected to make all relevant software available without restriction upon publication. If the original software is not able to be shared, authors must provide a reasonable licence.

Software manuscripts

Software submitted to the journal must meet the following requirements:

  • Based on open source standards.
  • Conform to the Open Source Definition.
  • Deposited in an open software archive (see Depositing software, below).
  • Included in the submission as supporting information.
  • Linked directly from the manuscript file.
Authors submitting software to the journal should also read these additional guidelines in addition to the policy details listed here.

Depositing Software

The following items must be deposited in an open software archive:

  • The associated source code of the software described in the manuscript. This should follow established community standards and be licensed under an open licence such as BSD, GPL, or MIT. The code should be easy to locate and download without creating user accounts or entering personal details.
  • Documentation for running and using the software. For end-user applications, instructions for installing and using the software are prerequisite; for software libraries, instructions for using the application program interface are prerequisite.
  • A test dataset with associated control parameter settings. Where feasible, results from standard test sets should be included. Where possible, test data should not have any dependencies.

Software Archives

Archives should provide a public repository of the described software. The repository must have been in existence for over five years or be hosting more than 1,000 projects.

Example archives

Reviewing Software Manuscripts

A software manuscript can be considered for publication if it covers a well-established project that has been providing an open source code repository for an extended amount of time.

In order for a software manuscript to be considered for publication, editors, reviewers, or readers must be able to:

  • Access the public version of the software.
  • Reproduce the results.
  • Run the software on the deposited dataset with the provided control parameters.

Software manuscripts will not be considered under the following circumstances:

  • They require access to databases or other resources whose persistence is not guaranteed.
  • Running the software depends on proprietary or otherwise unobtainable ancillary software.

Sharing Code

All researchers with submissions to the journal in which author-generated code underpins the findings are expected to make all author-generated code available without restriction upon publication. In cases where authors' code is central to the manuscript, the journal may require the code to be made available as a condition of publication. Authors are responsible for ensuring that the code is reusable and well-documented.

Recommendations for Sharing Code

Authors are encouraged to share their code in a way that follows best practice and facilitates reproducibility and reuse:

  • Share their code via a repository that issues persistent identifiers, such as DOIs.
  • Clearly licence their code using an open source licence.
  • Share clear documentation alongside the code that details any information needed to use the code — for example, dependencies.
  • State how the code can be accessed in the Data Availability Statement of their manuscript.

Code cannot be shared if there are legal or ethical reasons why authors should not do this; in the Data Availability Statement they should give details of how to request access to the code.

Contact

For questions about sharing materials, software, or code, please contact the Editorial Office.

Editorial Office — SAFE Journal of One Health
Published by The SAFE Society Publishing
Email: editor@thesafesociety.com
Website: https://journal.thesafesociety.com