Article type spotlight: Software Tool Articles
| 5 November, 2025 | Jack Nash |
At HRB Open Research, all research outputs deserve proper recognition. That’s why HRB Open Research publishes many diverse 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 data sets and include an example of the output that can be expected from the tool and how this output should be interpreted.
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 for analysis and interpretation makes reproducing your work easier for reviewers and readers. 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 HRB Open Research
Software Tool Articles published on HRB Open Research are available as citable publications. Below, we’ve highlighted some examples of Software Tool Articles published on the platform.
RxTrends: An R-based Shiny Application for Visualising Open Data on Prescribed Medications in Ireland
The Health Service Executive (HSE) in Ireland releases monthly reports on prescription dispensing claims and payments relating to community drug schemes. The above Software Tool presents RxTrends, an R-based Shiny application designed to visualize and analyze trends in prescribed medications in Ireland using data from HSE. It allows users to explore prescribing and cost trends for the most commonly prescribed medications, enhancing the practical value of the data for stakeholders such as researchers, healthcare professionals, and policymakers. The application includes functionalities for comparing medication usage and addressing various medication policy questions.
Read the full Software Tool Article.
GNOSIS: an R Shiny app supporting cancer genomics survival analysis with cBioPortal
Cancer diagnosis, classification and treatment generally follows an integrative approach combining clinical features and tissue-based biomarkers. In recent years, there has been an increased interest in using genetic testing to guide treatment decisions, predict patient response and determine likely prognoses for cancers associated with specific pathogenic variants. Such a precision oncology paradigm has been fostered by the extensive efforts of many cancer genomics consortia, yielding extraordinarily rich repositories of genomic and associated clinical data of hundreds to, in some cases, thousands of cancer patients.
Summary clinical and cancer genomic data are available from a number of consortia websites, with cBio Cancer Genomics Portal (cBioPortal) offering one of the best known and regularly accessed consolidated curations for multiple consortia; cBioPortal provides both graphical user interface (GUI)-based and representational state transfer (RESTful) mediated means for researchers to explore clinical and genomics data. However, cBioPortal’s exploratory capabilities have their limitations, requiring the implementation of a more sophisticated ‘off site’ analysis that typically requires significant prior programming experience.
The creators of the following Software Tool developed GNOSIS, an R Shiny app designed to assist users in exploring and visualizing cancer genomics data from the cBioPortal repository, enabling efficient survival analysis to identify prognostic markers. It features an intuitive interface with various functionalities, including data upload, visualization, and statistical analysis, while also promoting reproducible research through downloadable logs and scripts.
Read the full Software Tool Article.
Join other HRB Trust-funded authors already publishing Software Tool Articles, submit yours to HRB Open Research today.