Sharing research software: get the credit you deserve - F1000

Sharing research software: get the credit you deserve

5 mins


Software tools support research in almost every field of study, from DNA sequencing and disease modelling, to economic forecasting and digital humanities. However, these valuable software tools can often go unrecognized – the tool might get mentioned in the methods section of a research article, or a link to the software included in the footnotes. But is that really enough?  Discover how publishing a Software Tool Article can help you get the credit you deserve and support reproducibility in research.  

At F1000, we believe that all research outputs deserve proper recognition, including software tools and apps. We publish a wide range of article types – from the traditional research articles and reviews to more unusual formats such as Software Tool Articles, Data Notes, Case Reports, and beyond.   

We also know that reproducibility is the cornerstone of robust, trustworthy research. But so much published research is not reproducible for the simple fact that the authors haven’t fully shared the tools they used in their research, including the software they created as part of their work. This is where publishing your Software Tool Article comes in.   

What are Software Tool Articles?

Software Tool Articles offer researchers and software engineers a dedicated space to describe novel research software they have created, or tools which they have developed from existing software.   

The articles cover:  

  • Why the software was developed
  • Details of the code, method, and analysis
  • Examples of data input sets and outputs
  • Tips for other researchers on how to use and apply the tool

Software should be written in open access programming languages, and source code for new software must be made openly, permanently available in a repository like Zenodo.    

How do Software Tool Articles support reproducibility?  

Sharing research software, along with sample data, and guidance for analysis and interpretation, makes it easier for reviewers and readers to reproduce your research. Not only does this boost the credibility of your findings, but it also supports the wider movement towards reproducibility best practice in research.    

Why publish your Software Tool Article to an F1000 publishing venue?  

Software Tool Articles are fully citable and undergo peer review, meaning you can get the credit you deserve for all your research outputs. Once it’s passed peer review, your article will benefit from increased visibility through indexing in PubMed and Scopus. We welcome Software Tool Articles written in any open source programming language, including Python, R, and C, and our platforms supports code syntax highlighting, so that your code is fully readable in the body of your article.   

Here’s a rundown of some of the most impactful Software Tool Articles published on F1000Research to date: 

#1 epiflows: an R package for risk assessment of travel-related spread of disease [version 3; peer review: 2 approved] 

This article by Paual Moraga et al introduces R package epiflows, illustrating its use in assessing the risk of travel-related spread of yellow fever cases in Southeast Brazil. Included in both the Disease Outbreaks Gateway and the R Epidemics Consortium (RECON) Collection, this is a great example of a software tool with highly relevant and timely applications in safeguarding public health.  

This Software Tool Article makes excellent use of interactive figures via an iFrame, allowing readers to play with different visualizations, zoom in and out, filter the results, and dig into the details of the data for themselves within the article itself.

#2 FreeSASA: An open source C library for solvent accessible surface area calculations [version 1; peer review: 2 approved] 

Simon Mitternacht’s open source C library for solvent accessible surface area (SASA) calculations is highly configurable, allowing the user to control molecular parameters, accuracy, and output granularity. In this article, he introduces the library as a simple and fast command-line tool which is easily integrated into tool chains.  

This article showcases the proper support for code syntax highlighting:

#3 Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps [version 2; peer review: 2 approved]

This article from the ISCB Community Journal Gateway describes a web-based tool for researchers to build complex, high-quality clustered heat maps. Traditional heat maps are rich in data but static, so this web tool’s ability to produce next-generation heat maps supports a much more interactive and informative user experience.  

The Interactive CHM Builder is a perfect example of a software tool which can benefit and support future researchers due to its clear applications for research on genome-scale molecular profiling data in biology.  

#4 The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows [version 1; peer review: 2 approved]

This fascinating article from the Container Visualization in Bioinformatics Collection describes Dockstore, a project which brings together Docker images with standardized, machine-readable ways of describing the tools it contains. This supports the sharing and reuse of Docker-based tools and workflows for the genomics community.  

It’s a great example of the different types of tool that can be described in a Software Tool Article.

How to publish a Software Tool Article 

Software Tool Articles can be published to a range of F1000 publishing venues, Gateways, and Collections. The latter group together related content from communities, institutions, societies and more. Articles within Gateways and Collections benefit from increased visibility and allow communities a customizable publishing venue.   

We recently launched the Japan Institutional Gateway (JIG), which will feature work from researchers across the University of Tsukuba. Since launch, the Gateway has seen papers published across disciplines from telecollaboration to Covid responses and the Japanese constitution. 

What are the benefits of sharing your code and software openly?

Uncover how sharing software and code openly supports transparency, reproducibility, and reusability.