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data-anchor="loc-accessing-materials" name="loc-accessing-materials"><a href="#loc-accessing-materials"> Accessing materials </a></li> </ul></li> <li data-anchor="loc-sharing-software" name="loc-sharing-software"><a href="#loc-sharing-software"> Sharing Software </a> <ul> <li data-anchor="loc-software-manuscripts" name="loc-software-manuscripts"><a href="#loc-software-manuscripts"> Software manuscripts </a></li> <li data-anchor="loc-depositing-software" name="loc-depositing-software"><a href="#loc-depositing-software"> Depositing software </a></li> <li data-anchor="loc-software-archives" name="loc-software-archives"><a href="#loc-software-archives"> Software archives </a></li> <li data-anchor="loc-reviewing-software-manuscripts" name="loc-reviewing-software-manuscripts"><a href="#loc-reviewing-software-manuscripts"> Reviewing software manuscripts </a></li> </ul></li> <li data-anchor="loc-sharing-code" name="loc-sharing-code"><a href="#loc-sharing-code"> Sharing Code </a> <ul> <li data-anchor="loc-recommendations-for-sharing-code" name="loc-recommendations-for-sharing-code"><a href="#loc-recommendations-for-sharing-code"> Recommendations for sharing code </a></li> </ul></li> </ul> </nav> <article> <h1>Materials, Software and Code Sharing</h1> <div data-section-id="801"> <div class="block-global-alert"> The following policy applies to all PLOS journals, unless otherwise noted. </div> </div> <div data-section-id="721"> <div class="block-more-information"> <strong>Related policy: </strong><a href="/plosmedicine/s/data-availability">Data Availability</a> </div> </div> <div data-section-id="722"> <p>PLOS is committed to ensuring the availability of materials that underpin research. Sharing materials encourages reuse and facilitates reproducibility.</p> <p>PLOS reserves the right to issue a correction, expression of concern, or retraction if undisclosed restrictions on sharing are discovered after publication. PLOS will contact authors’ institutions and funders as appropriate.</p> <p>Our policy on availability does not require that materials must be made available free of charge.</p> </div> <div data-section-id="171"> <h2><a data-anchor-id="5259" id="loc-sharing-materials" name="loc-sharing-materials"></a>Sharing Materials</h2> <p>We expect that authors submitting to PLOS will make all relevant materials that may be reasonably requested by others available without restriction upon publication of the work. Where proportionate and justified restrictions exist, such as those intended to protect privacy or confidentiality of human research subjects, we expect their disclosure in the Materials and Methods section and a description of the conditions, if any, under which the materials may be accessed or used. Other acceptable grounds for restrictions can be found on page 11 of the <a href="https://unesdoc.unesco.org/ark:/48223/pf0000379949">UNESCO Recommendation on Open Science</a>.</p> <p>Editors and reviewers should verify the availability of materials during the peer review process, and contact the journal if any undisclosed restrictions are discovered.</p> <p>We strongly encourage authors to deposit copies of materials, including plasmids, cell lines, and model organisms, to established repositories. We support the use of any repository that meets <a href="/plosmedicine/s/recommended-repositories">our criteria</a>. We suggest utilizing <a href="https://fairsharing.org/">FAIRsharing</a>, the <a href="https://scicrunch.org/resources/about/resource">RRID Portal</a> or the Registry of Research Data Repositories (<a href="https://www.re3data.org/">Re3Data</a>) to find the most appropriate repository.</p> <p>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.</p> <h3><a data-anchor-id="7763" id="loc-research-resource-identifiers" name="loc-research-resource-identifiers"></a>Research Resource Identifiers</h3> <p>PLOS encourages authors to use Research Resource Identifiers (RRIDs) to cite and uniquely identify resources used in their research.</p> <p>The <a href="https://scicrunch.org/resources">RRID Portal</a> 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 in the text of their manuscripts to identify antibodies, plasmids, model organisms, cell lines, and tools, as shown in the following examples, which are linked to search results from the RRID Portal:</p> <ul> <li> <p><a href="https://scicrunch.org/resources/Any/search?q=undefined&l=RRID%3AAB_90755">RRID:AB_90755</a> (Antibody)</p></li> <li> <p><a href="https://scicrunch.org/resources/Plasmids/search?q=Addgene_44362&l=Addgene_44362">RRID:Addgene_44362</a> (Plasmid)</p></li> <li> <p><a href="https://scicrunch.org/resources/Any/search?q=MMRRC_026409-UCD&l=MMRRC_026409-UCD">RRID:MMRRC_026409-UCD</a> (Organism)</p></li> <li> <p><a href="https://scicrunch.org/resources/Any/search?q=undefined&l=RRID%3ACVCL_0033">RRID:CVCL_0033</a> (Cell Line)</p></li> <li> <p><a href="http://scicrunch.org/resolver/RRID:SCR_007358">RRID:SCR_007358</a> (Tool)</p></li> </ul> <p>See our <a href="/plosmedicine/s/best-practices-in-research-reporting">best practices for research reporting</a> for further details on reporting the use of specific research resources.</p> <h3><a data-anchor-id="5261" id="loc-accessing-materials" name="loc-accessing-materials"></a>Accessing materials</h3> <p><a data-parent-id="undefined" href="/plosmedicine/s/contact">Contact the journal</a> if you encounter difficulties obtaining materials associated with published articles.</p> <p>PLOS cannot arbitrate if any disputes arise, especially with respect to Material Transfer Agreements (MTAs). </p> </div> <div data-section-id="172"> <h2><a data-anchor-id="5262" id="loc-sharing-software" name="loc-sharing-software"></a>Sharing Software</h2> <p>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.</p> </div> <div data-section-id="723"> <h3 id="docs-internal-guid-0c8cfe2d-5c1d-db0b-fffa-9976453b614d"><a data-anchor-id="5263" id="loc-software-manuscripts" name="loc-software-manuscripts"></a>Software manuscripts</h3> <p>Software submitted to PLOS must meet the following requirements:</p> <ul> <li>Based on open source standards</li> <li>Conform to the <a href="http://www.opensource.org/docs/osd">Open Source Definition</a></li> <li>Deposited in an open software archive (see “Depositing software,” below)</li> <li>Included in the submission as supporting information</li> <li>Linked directly from the manuscript file</li> </ul> <p>If the software or algorithm is not central to the manuscript, we also encourage authors to make all relevant materials freely available.</p> </div> <div data-section-id="724"> <h3 id="docs-internal-guid-0c8cfe2d-5c1e-d5f2-8000-89f2d562ddbf"><a data-anchor-id="5264" id="loc-depositing-software" name="loc-depositing-software"></a>Depositing software</h3> <p>The following items must be deposited in an open software archive:</p> <ul> <li><strong>The associated source code of the software described in the manuscript.</strong> This should, as far as possible, follow accepted community standards and be licensed under a suitable license such as BSD, LGPL, or MIT (<a href="http://www.opensource.org/licenses/alphabetical">see the full list of suitable licenses</a>). 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.</li> <li><strong>Documentation for running and installing the software.</strong> 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.</li> <li><strong>A test dataset with associated control parameter settings.</strong> Where feasible, results from standard test sets should be included. Where possible, test data should not have any dependencies — for example, a database dump.</li> </ul> </div> <div data-section-id="725"> <h3 id="docs-internal-guid-474dd158-5c20-077e-a931-05964b81a0bd"><a data-anchor-id="5265" id="loc-software-archives" name="loc-software-archives"></a>Software archives</h3> <p>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.</p> <h4>Example archives</h4> <ul> <li><a href="http://sourceforge.net/">SourceForge</a></li> <li><a href="http://www.bioinformatics.org/">Bioinformatics.Org</a></li> <li><a href="http://www.open-bio.org/wiki/Main_Page">Open Bioinformatics Foundation (O|B|F)</a></li> <li><a href="http://savannah.gnu.org/">Savannah</a></li> <li><a href="https://github.com/">GitHub</a></li> </ul> </div> <div data-section-id="726"> <h3 id="docs-internal-guid-81021f1e-5c22-8a42-96bf-7c81cdcacdf3"><a data-anchor-id="5266" id="loc-reviewing-software-manuscripts" name="loc-reviewing-software-manuscripts"></a>Reviewing software manuscripts</h3> <p>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.</p> <p>In order for a software manuscript to be considered for publication, editors, reviewers, or readers must be able to:</p> <ul> <li>Access the public version of the software</li> <li>Reproduce the results</li> <li>Run the software on the deposited dataset with the provided control parameters.</li> </ul> <p>Only one hardware-software platform is required. The platform must be in common use by the readership (e.g., MATLAB).</p> <p>Software manuscripts will not be considered under the following circumstances:</p> <ul> <li>They require access to databases or other resources whose persistence is not guaranteed (e.g., individual laboratory databases without funding support).</li> <li>Running the software depends on proprietary or otherwise unobtainable ancillary software.</li> </ul> </div> <div data-section-id="2617"> <h2><a id="loc-sharing-code" name="loc-sharing-code" data-anchor-id="8407"></a>Sharing Code</h2> <p>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.</p> </div> <div data-section-id="2619"> <h3><a id="loc-recommendations-for-sharing-code" name="loc-recommendations-for-sharing-code" data-anchor-id="8408"></a>Recommendations for sharing code</h3> <p>Authors are encouraged to share their code in a way that follows best practice and facilitates reproducibility and reuse. Authors are encouraged to:</p> <ul> <li>Share their code via a repository that issues persistent identifiers, such as DOIs.</li> <li>Clearly license their code using an open source license. </li> <li>Share clear documentation alongside the code that details any information needed to run the code, for example dependencies.</li> <li>State how the code can be accessed in the Data Availability Statement of their manuscript. </li> </ul> </div> <div data-section-id="2620"> <p>More information on best practice for sharing code can be found in the <a data-parent-id="34" href="/plosmedicine/s/submission-guidelines#loc-methods-software-databases-and-tools"><i>PLOS Medicine</i> author guidance</a>.</p> </div> <div data-section-id="2621"> <p>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.</p> </div> </article> </div><script defer src="/resource/js/components/scroll.js" type="text/javascript"></script> <script defer src="/resource/js/components/floating_nav.js" type="text/javascript"></script> <script defer src="/resource/js/pages/site_content.js" type="text/javascript"></script> </main> <footer id="pageftr"> <div class="row"> <div class="block x-small"> <ul class="nav nav-secondary"> <li class="ftr-header"><a href="https://plos.org/publications/journals/">Publications</a></li> <li><a href="/plosbiology/" id="ftr-bio">PLOS Biology</a></li> <li><a href="/climate/" id="ftr-climate">PLOS Climate</a></li> <li><a href="/complexsystems/" id="ftr-complex-systems">PLOS Complex Systems</a></li> <li><a href="/ploscompbiol/" id="ftr-compbio">PLOS Computational Biology</a></li> <li><a href="/digitalhealth/" id="ftr-digitalhealth">PLOS Digital Health</a></li> <li><a href="/plosgenetics/" id="ftr-gen">PLOS Genetics</a></li> <li><a href="/globalpublichealth/" id="ftr-globalpublichealth">PLOS Global Public Health</a></li> </ul> </div> <div class="block x-small"> <ul class="nav nav-secondary"> <li class="ftr-header"> </li> <li><a href="/plosmedicine/" id="ftr-med">PLOS Medicine</a></li> <li><a href="/mentalhealth/" id="ftr-mental-health">PLOS Mental Health</a></li> <li><a href="/plosntds/" id="ftr-ntds">PLOS Neglected Tropical Diseases</a></li> <li><a href="/plosone/" id="ftr-one">PLOS ONE</a></li> <li><a href="/plospathogens/" id="ftr-path">PLOS Pathogens</a></li> <li><a href="/sustainabilitytransformation/" id="ftr-sustainabilitytransformation">PLOS Sustainability and Transformation</a></li> <li><a href="/water/" id="ftr-water">PLOS Water</a></li> </ul> </div> <div class="block xx-small"> <ul class="nav nav-tertiary"> <li> <a href="https://plos.org" id="ftr-home">Home</a> </li> <li> <a href="https://blogs.plos.org" id="ftr-blog">Blogs</a> </li> <li> <a href="https://collections.plos.org/" id="ftr-collections">Collections</a> </li> <li> <a href="mailto:webmaster@plos.org" id="ftr-feedback">Give feedback</a> </li> <li> <a href="/plosmedicine/lockss-manifest" id="ftr-lockss">LOCKSS</a> </li> </ul> </div> <div class="block xx-small"> <ul class="nav nav-primary"> <li><a href="https://plos.org/privacy-policy" id="ftr-privacy">Privacy Policy</a></li> <li><a href="https://plos.org/terms-of-use" id="ftr-terms">Terms of Use</a></li> <li><a href="https://plos.org/advertise/" id="ftr-advertise">Advertise</a></li> <li><a href="https://plos.org/media-inquiries" id="ftr-media">Media Inquiries</a></li> <li><a href="https://plos.org/contact" id="ftr-contact">Contact</a></li> </ul> </div> </div> <div class="row"> <p> <img src="/resource/img/logo-plos-footer.png" alt="PLOS" class="logo-footer"/> <span class="footer-non-profit-statement">PLOS is a nonprofit 501(c)(3) corporation, #C2354500, based in San Francisco, California, US</span> </p> <div class="block"> </div> </div> <script src="/resource/js/global.js" type="text/javascript"></script> </footer> </body> </html>