Article Type Spotlight: Software Tool Articles

At Gates Open Research, all research outputs deserve proper recognition. That’s why Gates Open Research publishes a diverse range of article types, from traditional Research Articles to less common formats such as Software Tool Articles, Data Notes, and beyond.

In this blog, we outline what a Software Tool Article is and how publishing one could increase recognition and improve the visibility and impact of your research.

What are Software Tool Articles?

Software Tool Articles are research outputs that enable researchers and software engineers to describe their research software or tools developed from existing software. They should include the rationale for the development of the tool and details of the code used for its construction. The article should provide examples of suitable input datasets and include an example of the output that can be expected from the tool, along with guidance on how to interpret it. 

Why should I publish a Software Tool Article as part of my research project?

Much published research isn’t reproducible because authors haven’t fully shared the tools they used, including the software they created. Software Tool Articles aim to solve this issue. Sharing research software, sample data, and guidance on analysis and interpretation makes it easier for reviewers and readers to reproduce your work. This improves the credibility of your findings and promotes the wider movement toward reproducibility best practices in research.

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 Platform supports code syntax highlighting, so your code is fully readable in the body of your article.

Software Tool Articles on Gates Open Research

Software Tool Articles published on Gates Open Research are available as citable publications. Below, we’ve highlighted some examples of Software Tool Articles published on the platform.

Introducing QRLabelr: Fast user-friendly software for machine- and human-readable labels in agricultural research and development

The open-source software QRLabelr has been developed to address a key challenge in agricultural research: creating field plot labels that are both machine- and human-readable. These labels play a vital role in modern experiments, particularly those involving digital data collection and advanced phenotyping techniques. Unlike commercial software, which can be prohibitively expensive for underfunded research programs, QRLabelr is freely available, making it an invaluable resource for researchers in developing countries. Designed as an R package, it offers flexible, customizable features for generating labels, while an interactive Shiny app ensures accessibility for users with little or no R programming experience. By enabling accurate QR encoding, faster label creation, and improved data tracking, QRlabelr supports best practices in agricultural research, helping scientists streamline their workflows and enhance the reliability of their experiments.

Read the full Software Tool article here.

TitrationAnalysis: a tool for high throughput binding kinetics data analysis for multiple label-free platforms

TitrationAnalysis is a new high-throughput analysis tool designed to streamline the study of biomolecular interactions using label-free techniques like Surface Plasmon Resonance SPR and Biolayer Interferometry BLI. These techniques are widely used to measure binding kinetics, such as how molecules associate and dissociate during interactions. Built as a package for the Mathematica scripting environment, TitrationAnalysis uses advanced non-linear curve-fitting to automatically analyze binding data and calculate key metrics like association rate (ka), dissociation rate (kd), and dissociation constant (KD).

The tool is user-friendly, requiring minimal knowledge of Mathematica scripting, and works seamlessly with data from multiple platforms, including Biacore T200, Carterra LSA, and ForteBio Octet Red384. Additionally, TitrationAnalysis offers customizable output formats, making it ideal for downstream data quality control in compliance with Good Clinical Laboratory Practice standards. With its flexibility and efficiency, TitrationAnalysis provides researchers with a powerful and accessible alternative for characterizing biomolecular interactions.

Read the full Software Tool article here.

Join other Gates Foundation-funded authors already publishing Software Tool Articles, submit yours to Gates Open Research today.