Code Sharing Guidance

Data Availability Statement Examples

Below are some example statements that illustrate how you might wish to describe the location of the data and code in your manuscript.

Where code is shared:

The alligned Illumina sequencing data are deposited in the NCBI short read archive under the Bioproject accession PRJNA681155. The processed data used to generate figures and statistics in the test, the data from growth rate assays, simulation code and data and analysis scripts are available on Zenodo: 10.5281/zenodo.3787242.

All data and R code files are available through Open Science Framework (https://doi.org/10.17605/OSF.IO/K5FJE).

There are no primary data in the paper; all materials are available at https://github.com/bbolker/HIV_LHS/ and we have archived our code on Zenodo (DOI: 10.5281/zenodo.437497).

Where code cannot be openly shared:

Access to the code used within this paper is available to bona fide researchers via academic partnership with UKHSA. More information on partnership with the agency is available at https://research.ukhsa.gov.uk/partnerships/ and initial contact may be made via ResearchSupport@ukhsa.gov.uk.

All transcriptomics data used for drug predictions can be accessed through the Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or Open Science Framework (https://osf.io/7nrd3/) using the identifiers indicated in Table 1. The NeMoCAD code is stored on Zenodo (https://doi.org/10.5281/zenodo.7692712) and access can be requested by submitting the S1 Form to the Data Manager, Wyss Institute for Biologically Inspired Engineering at Harvard University (email: Info@wyss.harvard.edu). The Cerner patient data analyzed in this study is subject to the following licenses/restrictions: This was an observational study of electronic health records that cannot be made publicly available. Requests to access these datasets should be directed to the Cerner Clinical Research Team, coviddatalab@cerner.com.

Further Information and Support

When did this policy come into effect?

This policy was launched on 1 January 2026 and applies to all new manuscripts submitted to PLOS Biology.

How does the code sharing policy on PLOS Biology relate to the data and software sharing policies?

This policy complements the existing Data Sharing and Software Sharing policies. PLOS Biology already requires that any underlying data that is needed to replicate the study' s findings should be made openly available and has previously noted an expectation for authors to make their code and software openly available. We now require all author-generated code directly related to their study’s findings to be made available. The Software Sharing policy is specifically for manuscripts describing new software.

Will the reviewers look at my code?

The code sharing policy does not change the way reviewers will assess your manuscript. If there are limitations on your ability to share the code, this should be outlined in the cover letter on initial submission and it will be subject to staff and/or editorial assessment. When code is shared, reviewers are encouraged to look at the code but are not required to include it in their review. We recommend that code central to the findings should be shared on submission either publicly or privately with the reviewers and editors for their assessment as necessary. It is the authors’ responsibility to ensure that the code is of sufficient quality.

My code has many dependencies and I think this will make sharing it meaningless. What do you suggest I do?

If you want to go further than describing your code’s dependencies, and render your code reusable for a longer period of time then you could consider using a container to package your code along with any dependencies in the environment it was created to run in. Examples of container technology are Code Ocean, Binder and Docker. You will need to ensure that any dependencies allow for redistribution in this way.

What license should I give my code?

You are free to choose whatever license you wish, although PLOS Biology strongly recommends a license that supports open, reproducible research. If you chose to apply an open source license to your code and need help deciding on which license to use, you might find the Choose a Licence website useful. Please note, Creative Commons licenses are not recommended for code or software.

 

Before selecting a license for your code, be sure to take into consideration any third party obligations that may apply, for example: any license that may apply to third party code used by you (if applicable), the policies of your institution, funder and collaborators.

When should I share?

Your code must be publicly available at the time of publication of the article and available for peer review; however, it does not need to be publicly available at the peer review stage. Some repositories, such as Github, figshare or Code Ocean, will allow you to share your work with others privately. You should include private links in the cover letter.

What if I cannot provide a DOI for my code at submission?

If the code is uploaded to a repository that issues DOIs (or other permanent identifiers) only at publication, authors may submit their manuscript and include placeholder language in their Data Availability Statement indicating that the DOI/identifier will be made available after acceptance. The journal office will contact authors prior to publication to ask for this information and will hold the manuscript until it is received.

 

Providing private code access to reviewers and editors during the peer review process is acceptable. Many repositories permit private access for review purposes, and have policies for public release at publication.

How do I share my code well?

Your code should be well described and documented in order to facilitate others reusing it or running it. Repositories will usually require certain information to be entered when you submit your code but the more information you add the more useful your code becomes. Including a README file is regarded by many as a basic requirement to share alongside your code. You should ensure that you describe the environment in which your code should be run and any dependencies there are. You should also state the version of the code you are sharing and a link to live code so users can check for any updates. Including a LICENSE.txt file which specifies the copyright holder and terms under which others can use, modify and share your code is a good idea. Within your code, annotation is very important as it helps others understand what you are aiming to achieve. For more information on describing your code see The Software Sustainability Institute’s guide Software deposit: how to describe a software deposit.

Are there any guidelines on how to share research using machine learning or AI techniques?

Some community-derived guidelines do exist and some provide checklists as to what you should share. The following resources may be helpful:

• DOME-ML (Community Standard for Transparent Machine Learning) - https://dome-ml.org/
• Heil et al. (2021) Reproducibility standards for machine learning in the life sciences. Nature Methods, DOI:10.1038/s41592-021-01256-7

How should I link my data to my code?

The location of both your data and code should be stated in your Data Availability Statement. In addition you can add information to both the data and code repository records detailing the associated article and other supporting outputs (data or code). If the repository does not have a dedicated field to add this information to, then you should cite the data or code using citation best practice guidelines.

Should my data and code be shared in the same place?

There is no requirement for your data and code to be in the same place. It is possible that they are more suited to different repositories and you should use domain specific repositories whenever possible.

My institution/funder/employer retains the IP of the code I produce. Can I publish in PLOS Biology​?

If there are contractual obligations, local regulations, legal or ethical reasons why you cannot share code these should be shared with the journal who will assess whether it can be exempted from this policy. Please also check the policy of your institution/funder/employer carefully as some may make exceptions for sharing code or software for scientific advancement. PLOS Biology does not require you to use a certain license and applying an “all rights reserved” license may satisfy your institutional/funder requirements. If you need to share your code with a specific license you should use a permanent repository that offers the correct licence as Supporting Information is not suitable.

What happens if I want to commercialise the code in the future?

This policy does not prohibit you from commercialising your code.

 

 

External Link Disclaimer

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