Software tool articles: A guide for researchers
Introduction to new article types
Understanding software tool articles
A software tool article is a peer reviewed article type. It describes the rationale for the development of a new software tool and details of the code used for its construction. The article should provide examples of suitable input data sets and include an example of the output that can be expected from the tool and how this output should be interpreted.
What are the benefits of publishing a software tool?
Publishing a software tool allows you to:
Maximize the potential of your research code and software through improving the discoverability, usability, and reproducibility of your research
Gain appropriate credit for your code and software with a citable publication
Reach new audiences for your research to increase the findability of your research
Foster new collaborations across disciplines by helping others to find and use your code and software
How do I write a software tool article?
A software tool article describes the rationale for the development of a new software tool and details of the code used for its construction.
The article should provide examples of suitable input data sets and include an example of the output that can be expected from the tool and how this output should be interpreted. Software tool articles should be written in open source programming languages.
Software Tools typically contain the following sections:
Abstract
Read tips on writing your abstract.
Keywords
Read making your article more discoverable, including information on choosing a title and search engine optimization.
Main body
Introduction
Provide context as to why the software tool was developed and what need it addresses. It is good scholarly practice to mention previously developed tools that address similar needs, and why the current tool is needed.
Methods
Include a subsection on Implementation describing how the tool works and any relevant technical details required for implementation; and a subsection on Operation, which should include the minimal system requirements needed to run the software and an overview of the workflow.
Results (optional)
This section is only required if the paper includes novel data or analyses and should be written as a traditional results section.
Use cases (optional)
Please include a section on Use cases if the paper does not include novel data or analyses. Examples of input and output files should be provided with some explanatory context. Any novel or complex variable parameters should be explained in sufficient detail to enable users to understand and use the tool’s functionality.
Conclusions/Discussion
This section should include a discussion of the results (e.g. if the paper includes novel data or analyses) or conclusions should include a brief discussion of allowances made (if any) for controlling bias or unwanted sources of variability, and the limitations of any novel datasets.
Declaration of interest statement
This is to acknowledge any financial or non-financial interest that has arisen from the direct applications of your research. Further guidance on what is a conflict of interest and how to disclose it.
Data availability
Authors of software tools are required to provide a data availability statement (DAS), detailing where data associated with a paper can be found and how it can be accessed. If data cannot be made open, authors should state why in the data availability statement. This should include the hyperlink, DOI or other persistent identifier associated with the data set(s). Templates are also available to support authors.
Software and code availability
Authors must include a software availability statement, which authors should add to the end of the article, before the references list.
Authors must make the source code available on a Version Control System (VCS) such as GitHub and provide details of the repository and the license under which the software can be used. Please also deposit an archived copy of the software at the time of submission to a recognized repository. You should include a statement in the manuscript as follows:
Software available from: URL for the website where software can be downloaded from
Source code available from: URL for versioning control system (for example GitHub)
Archived source code at time of publication: DOI and citation for project (for example in Zenodo). Please select the appropriate DOI for the version which underlies your article
License: Must be an open license and preferably an OSI-approved license
Code and software should be cited in the body of your article, be added to your reference list as you would any other bibliographic citation. Further guidance for sharing research code and software can be found here.
References
You must reference all sources, including your data, code and software.
Tables and figures
Figures should be supplied in one of our preferred file formats: PS, JPEG, TIFF, or Microsoft Word (DOC or DOCX) files are acceptable for figures that have been drawn in Word. For information relating to other file types, please consult our Submission of electronic artwork.
Tables should present new information rather than duplicating what is in the text. Readers should be able to interpret the table without reference to the text.
Further resources
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