Software Availability Statement
Table of Contents
A “Software Availability” statement provides information about software tools that were either used or created as part of a research project or which may be required to view datasets or replicate the analysis. This statement provides information such as the name of the software, links to where the software or source code is available, persistent identifiers for the software (such as a DOI or SWHID), version of the software, licensing information, and alternative software that may be used instead. This special section usually has a title like “Software Availability” or “Code Availability”.
If a software availability statement is present in an article, it should be tagged as a section and the <sec> element should have attribute sec-type="software-availability".
Any research article may contain a Software Availability statement, although articles that have article type “Software Tool Article” (article-type="software-tool-article") are expected to contain a Software Availability statement.
Each piece of software that is described in the Software Availability statement should be included in the references list of the article. References to software should have attribute publication-type="software" on the <mixed-citation> element. A callout to the software reference should be tagged using <xref>. If the references list of an article is missing a reference for software that is described in the Software Availability statement, or if a callout to such a reference is missing, this typically should not be corrected by typesetters; instead, if possible, a query should be raised for the author or editor.
The <sec> element for a Software Availability Statement should be placed directly within the <back> element.
If a Data Availability statement is also present, the Software Availability statement typically should be placed after the Data Availability statement. The Software Availability statement typically should not be combined with the Data Availability statement. However, if a combined Data and Software Availability statement that describes data and software is provided the @sec-type attribute can contain both identifiers separated by a space, sec-type="data-availability software-availability".
This example shows a Software Availability statement and a reference to the software that is described. Note there can be variations arising from the information provided by the author and the journal’s reference style (this example uses APA style).
Key points:
- The Software Availability statement is identified by attribute
sec-type="software-availability" - The Software Availability statement is located directly within <back>.
- The reference is identified as a software citation by
publication-type="software" - The Software Availability statement contains an <xref> element linking to the software citation, and contains an <ext-link> element linking to where the software is available.
<back>
<sec sec-type="software-availability">
<title>Software Availability</title>
<p>The sentiment analysis was conducted using <xref ref-type="bibr" rid="CIT0148">Stanford CoreNLP</xref>, version 3.9.2, available from <ext-link ext-link-type="uri" xlink:href="https://github.com/stanfordnlp/CoreNLP">https://github.com/stanfordnlp/CoreNLP</ext-link>.</p>
</sec>
<ref-list>
<ref id="CIT0148">
<mixed-citation publication-type="software"><source><italic>Stanford CoreNLP</italic></source> (Version <version>3.9.2</version>) [<comment>Computer software</comment>]. (<year>2018</year>). <ext-link ext-link-type="uri" xlink:href="http://nlp.stanford.edu/software/stanford-corenlp-full-2018-10-05.zip">http://nlp.stanford.edu/software/stanford-corenlp-full-2018-10-05.zip</ext-link></mixed-citation>
</ref>
</ref-list>
</back>This example shows parts of a Software Tool Article (https://doi.org/10.12688/f1000research.4460.1) to illustrate the Software Availability statement, article type, section heading, and software citation.
Key points:
- The article type Software Tool Article is specified in
article-type="software-tool-article"and<subj-group subj-group-type="article-type"><subject>Software Tool Article</subject><subj-group> - The section heading specified in
<subj-group subj-group-type="heading"><subject>is also “Software Tool Article” although the section heading may be different than the article type. - The Software Availability statement is identified by attribute
sec-type="software-availability" - The Software Availability statement is located directly within <back>.
- The reference is identified as a software citation by
publication-type="software" - The Software Availability statement contains an <xref> element linking to the software citation, <ext-link> elements linking to where the software is available, and license information for the software.
<article article-type="software-tool-article">
<front>
<article-meta>
<article-id pub-id-type="doi">10.12688/f1000research.4460.1</article-id>
<article-categories>
<subj-group subj-group-type="article-type">
<subject>Software Tool Article</subject>
</subj-group>
<subj-group subj-group-type="heading">
<subject>Software Tool Article</subject>
</subj-group>
</article-categories>
</article-meta>
</front>
<back>
<sec sec-type="software-availability">
<title>Software availability</title>
<p>Software available from:
<ext-link ext-link-type="uri"
xlink:href="http://apps.cytoscape.org/apps/enhancedGraphics"
>http://apps.cytoscape.org/apps/enhancedGraphics</ext-link>
</p>
<p>Latest source code:
<ext-link ext-link-type="uri"
xlink:href="https://github.com/RBVI/enhancedGraphics"
>https://github.com/RBVI/enhancedGraphics</ext-link>
</p>
<p>Source code as at the time of publication:
<ext-link ext-link-type="uri"
xlink:href="https://github.com/F1000Research/enhancedGraphics/releases/tag/v1"
>https://github.com/F1000Research/enhancedGraphics/releases/tag/v1</ext-link>
</p>
<p>Archived source code as at the time of publication:
<ext-link ext-link-type="doi"
xlink:href="https://doi.org/10.5281/zenodo.10421"
>https://doi.org/10.5281/zenodo.10421</ext-link>
<sup>
<xref ref-type="bibr" rid="ref-11">11</xref>
</sup>
</p>
<p>Software license: Lesser GNU Public License 3.0:
<ext-link ext-link-type="uri"
xlink:href="https://www.gnu.org/licenses/lgpl.htmlM"
>https://www.gnu.org/licenses/lgpl.htmlM</ext-link>
</p>
</sec>
<ref-list>
<ref id="ref-11">
<label>11</label>
<mixed-citation publication-type="software">
<person-group person-group-type="author">
<string-name><surname>Morris</surname>
<given-names>JH</given-names></string-name>,
<string-name><surname>Kuchinsky</surname>
<given-names>A</given-names></string-name>,
<string-name><surname>Ferrin</surname>
<given-names>TE</given-names></string-name>
<etal><italic>et al.</italic></etal></person-group>:
<article-title>F1000Research/enhancedGraphics</article-title>.
<source><italic>ZENODO</italic></source>.
<year>2014</year>.
<pub-id pub-id-type="doi"
>https://doi.org/10.5281/zenodo.10421</pub-id>
</mixed-citation>
</ref>
</ref-list>
</back>
</article>
Software Availability statements generally describe software that is available on a repository or website that is separate from the article, as shown in the examples above, however, it is also possible that an author may provide a Software Availability statement and include software or code as supplementary material for the article. This example, which is not typical, shows a Software Availability statement which states that the software is available in the article’s supplementary online material, provides a link to the supplementary material using the article’s DOI, and uses an endnote to link to software that is available on a repository.
Key points:
- The Software Availability statement is identified by attribute
sec-type="software-availability" - The Software Availability statement is located directly within <back>.
- The article’s DOI is used to link to the supplementary material.
- The supplementary material files are referenced in the usual way using the <supplementary-material> element and linked in a Supplementary Material section.
- The author has used a footnote, instead of a reference, to provide information about where software is available so the <xref> points to the footnote. (Using references is typically preferred over footnotes but this can vary depending on journal style, however footnotes do not provide the same functionality for citation metrics as references.)
<article>
<front>
<article-meta>
<article-id pub-id-type="doi">10.1080/09524622.2023.2259327</article-id>
<supplementary-material id="SM9868" mimetype="text/x-python" xlink:href="TBIO_A_2259327_SM9868.py"><caption><title>plot_formant_triangles.py</title></caption></supplementary-material>
<supplementary-material id="SM9859" mimetype="text/x-python" xlink:href="TBIO_A_2259327_SM9859.py"><caption><title>generate_playbacks.py</title></caption></supplementary-material>
<supplementary-material id="SM9852" mimetype="text/x-python" xlink:href="TBIO_A_2259327_SM9852.py"><caption><title>calculate_pitch.py</title></caption></supplementary-material>
</article-meta>
</front>
<back>
<fn-group>
<title>Notes</title>
<fn id="en0001" fn-type="endnote"><label>1. </label><p>Available from <ext-link ext-link-type="uri" xlink:href="https://github.com/YannickJadoul/Parselmouth" >https://github.com/YannickJadoul/Parselmouth</ext-link></p>
</fn>
</fn-group>
<sec sec-type="software-availability">
<title>Software Availability</title>
<p>The code described in this article is available in the supplementary online material available at <ext-link ext-link-type="doi" xlink:href="https://doi.org/10.1080/09524622.2023.2259327" >https://doi.org/10.1080/09524622.2023.2259327</ext-link> under a <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">CC BY 4.0</ext-link> license. This code requires having <xref rid="en0001" ref-type="fn">Parselmouth</xref> installed.</p>
</sec>
<sec sec-type="supplementary-material">
<title>Supplementary material</title>
<p>Supplemental data for this article can be accessed online at <ext-link ext-link-type="doi" xlink:href="https://doi.org/10.1080/09524622.2023.2259327">https://doi.org/10.1080/09524622.2023.2259327</ext-link></p></sec>
</back>
</article>