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At Wellcome Open Research, all research outputs deserve proper recognition. That’s why Wellcome 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 Wellcome Open Research

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

GRAPEVNE – Graphical Analytical Pipeline Development Environment for Infectious Diseases

The increase in volume and diversity of relevant data on infectious diseases and their drivers provides opportunities to generate new scientific insights that can support ‘real-time’ decision-making in public health across outbreak contexts and enhance pandemic preparedness. However, utilising the vast array of clinical, genomic, epidemiological, and spatial data collected globally is difficult due to differences in data preprocessing, data science capacity, and access to hardware and cloud resources.

GRAPEVNE is an open-source graphical analytical pipeline development environment designed to facilitate large-scale and routine analyses of infectious disease data at the local level, enhancing public health decision-making and pandemic preparedness. Built on the Snakemake workflow management system, it allows users to create modular pipelines for complex data analysis workflows, supporting various scientific applications and promoting reproducibility in research.

Read the full Software Tool Article here.

AnoPrimer: Primer Design in malaria vectors informed by range-wide genomic variation

The major malaria vector species, Anopheles gambiae s.l and Anopheles funestus, are some of the most studied organisms in medical research and also some of the most genetically diverse. Relational primer and probe design is crucial when designing polymerase chain reaction (PCR) or hybridisation-based molecular assays.

AnoPrimer is a Python package designed to facilitate the rapid design of primers and probes for these malaria vectors, taking into account their significant genetic diversity. It utilises the Ag1000G and Af1000 datasets to summarise genetic variation in primer binding sites and is accessible through Google Colaboratory, making it a valuable resource for researchers in the field.

Read the full Software Tool Article here.

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