Materials, Software and Code Sharing
PLOS is committed to ensuring the availability of materials that underpin research. Sharing materials encourages reuse and facilitates reproducibility.
PLOS reserves the right to issue a correction, expression of concern, or retraction if unreasonable restrictions on sharing are discovered after publication. PLOS will contact authors’ institutions and funders as appropriate.
Our policy on availability does not require that materials must be made available free of charge.
We expect that all researchers submitting to PLOS will make all relevant materials that may be reasonably requested by others available without restrictions upon publication of the work.
Editors and reviewers should verify the availability of materials during the peer review process, and contact the journal if any restrictions are discovered.
We strongly encourage authors to deposit copies of materials, including plasmids, cell lines, and model organisms, to established repositories such as Addgene, American Type Culture Collection, Arabidopsis Biological Resource Center, Bloomington Drosophila Stock Center, Caenorhabditis Genetics Center, DSMZ, European Conditional Mouse Mutagenesis Program, European Mouse Mutant Archive, Knockout Mouse Project, Jackson Laboratory, Mutant Mouse Regional Resource Centers, PlasmID, and RIKEN Bioresource Centre. While these examples may be specific to the life sciences, we expect all relevant materials to be deposited to relevant repositories, whenever possible, across all fields of research.
Research resource identifiers
As part of the Resource Identification Initiative, a cross-publisher effort to enable effective tracking of research resources and promote reproducibility, PLOS encourages authors to use Research Resource Identifiers (RRIDs) for citing and uniquely identifying resources used in the research.
The RRID Portal provides a searchable database of existing RRIDs and includes instructions for creating new ones if an RRID does not already exist. Authors should include RRIDs within the text of their papers to identify antibodies, plasmids, model organisms, cell lines, and tools, as shown in the following examples, which are linked to meta-data from the RRID Portal:
RRID:AB_90755 (Antibody) - If the antibody is commercially obtained, also report the lot number.
RRID:CVCL_0033 (Cell Line)
Exceptions to sharing materials
Materials should not be shared if they compromise the privacy or confidentiality of human research subjects, and authors should include a statement in their Materials and Methods discussing any restrictions on availability or use.
Contact the journal if you encounter difficulties obtaining materials from published articles.
PLOS cannot arbitrate if any disputes arise between authors and peer review participants, especially in terms of Materials Transfer Agreements (MTAs).
We expect that all researchers submitting to PLOS submissions in which software is the central part of the manuscript will make all relevant software available without restrictions upon publication of the work. Authors must ensure that software remains usable over time regardless of versions or upgrades. If the original software is not able to be shared, authors must provide a reasonable facsimile.
Software submitted to PLOS 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
If the software or algorithm is not central to the manuscript, we also encourage authors to make all relevant materials freely available.
The following items must be deposited in an open software archive:
- The associated source code of the software described in the manuscript. This should, as far as possible, follow accepted community standards and be licensed under a suitable license such as BSD, LGPL, or MIT (see the full list of suitable licenses). Dependency on commercial software such as Mathematica and MATLAB does not preclude a manuscript from consideration, although complete open source solutions are preferred. The code should be easy to locate and download without creating user accounts, logging in, or entering other personal details.
- Documentation for running and installing 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 — for example, a database dump.
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.
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.
Only one hardware-software platform is required. The platform must be in common use by the readership (e.g., MATLAB).
Software manuscripts will not be considered under the following circumstances:
- They require access to databases or other resources whose persistence is not guaranteed (e.g., individual laboratory databases without funding support).
- Running the software depends on proprietary or otherwise unobtainable ancillary software.
We expect all researchers with submissions to PLOS in which author-generated code underpins the findings in the manuscript to make all author-generated code available without restrictions upon publication of the work. In cases where code is central to the manuscript, we 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. Authors are encouraged to:
- Share their code via a repository that issues persistent identifiers, such as DOIs.
- Clearly license their code using an open source license.
- Share clear documentation alongside the code that details any information needed to run the code, for example dependencies.
- State how the code can be accessed in the Data Availability Statement of their manuscript.
More information on best practice for sharing code can be found in the PLOS Genetics author guidance.
If code cannot be shared due to legal or ethical reasons then authors should state this in the Data Availability Statement and give details of how to request access to the code. In cases where code can not be publicly shared, editors and reviewers reserve the right to access the code if deemed necessary for full assessment of the manuscript.