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Vicky Hellon, Associate Publisher at F1000 Research Ltd introduces our latest call for papers by highlighting some of the best software tool articles on our open research publishing platform F1000Research. Discover how publishing one of these articles can help you get the credit you deserve and support reproducibility in research. 

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?  

At F1000 Research, we believe that all research outputs deserve proper recognition, including software tools. That’s why 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, such as software they created as part of their work. This is where publishing your software tool article comes in.  

Keep reading to find out more about software tool articles, and why F1000Research is the perfect home for this unique type of research output. 

What are software tool articles? 

Software tool articles on F1000Research 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 on F1000Research? 

F1000Research is the perfect home for your software tool article. 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 tools 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.  

There’s more information about the benefits of the F1000Research platform and model on our software tool articles homepage, but don’t just take our word for it. Here’s a rundown of some of the best software tool articles published on F1000Research to date, which really showcase the benefits of the platform for this type of article:

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 which F1000Research facilitates: 

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 which can be described in a software tool article – F1000Research welcomes articles on a wide range of tools, from this Docker-based project to web apps, algorithms, packages and more. 

What are people saying about software tools? 

Software tools articles are growing in popularity with researchers, and the tools they describe are equally valuable in supporting and conducting research across a range of fields. It’s no wonder that the research community has a lot to say about software – which is why we also publish opinion articles and reviews, which explore different facets of research software including recommendations and best practice guidelines for software engineers.  

• Top 10 metrics for life science software good practices [version 1; peer review: 2 approved] 
• Four simple recommendations to encourage best practices in research software [version 1; peer review: 3 approved] 
• Recommendations for the packaging and containerizing of bioinformatics software [version 2; peer review: 2 approved, 1 approved with reservations] 
• Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action [version 1; peer review: 3 approved] 
• General guidelines for biomedical software development [version 2; peer review: 2 approved] 

What next? 

Software tool articles can be featured in our associated gateways and collections, which group together related content from communities, institutions, societies and more. Articles within gateways and collections benefit from increased visibility, and allow communities a customizable hub as a publishing venue.  

We have recently launched the NEUBIAS gateway, which will feature a broad range of content on image data analysis and promote knowledge sharing as well as ensuring credit for Bioimage analysts.  

Also new to F1000Research is the CABANA collection which will feature assets and articles from the CABANA project, which aims to strengthen capacity for bioinformatics research and training in Latin America.  

We also plan to participate in a cross-publisher working group later this year, exploring best practice for incorporating code review within the peer review process for software tool articles and beyond. If you have any ideas for any new initiatives or projects like this which F1000Research could be involved with, get in touch at publishers@f1000.com.  

Find out more about the benefits of publishing your software tool article on F1000Research, and submit your paper today.