From Code to Clicks: Building Interactive and Reproducible Bioinformatics Applications

Bioinformatics increasingly depends on reproducible workflows, open data, and software that can be shared beyond the laboratories in which it was developed. However, transforming an analysis into a reliable, maintainable, and accessible application remains challenging. Interactive tools must address not only scientific validity, but also software architecture, interface design, documentation, testing, deployment, provenance, and long-term sustainability. Frameworks such as R Shiny, Python Shiny, Dash, Streamlit, and Observable enable users to explore data, modify parameters, visualize results, and generate reports without directly editing code. Nevertheless, interactivity does not guarantee reproducibility, usability, accessibility, or technical quality. These frameworks sit within a broader ecosystem: notebook-based and literate environments (e.g., Jupyter, Quarto) support interactive, reproducible analyses; workflow management systems (e.g., Nextflow, Snakemake, Galaxy, CWL) provide the execution and orchestration layer; and container and dependency tools underpin portability. Connecting these layers into applications usable by end users without an informatics background requires further research and deliberate design approaches. Current work continues to examine how application design can support transparent decision-making. Relevant application domains span genomics, transcriptomics, proteomics, metagenomics, clinical bioinformatics, structural biology, and related disciplines. Important gaps remain in the comparative evaluation of frameworks, user-centered design, software sustainability, auditability, and evidence of adoption beyond individual projects.This Research Topic aims to advance the design, implementation, evaluation, deployment, and sustainability of end-user-facing interactive bioinformatics software. It will encourage contributions that translate computational methods and datasets into reusable applications, packages, platforms, and community resources. The Topic will examine how software architecture, interface design, validation, documentation, provenance, and deployment strategies influence scientific reproducibility and user experience. It will also consider how collaboration among bioinformaticians, research software engineers, developers, and end users can improve the reliability, accessibility, maintainability, and impact of interactive tools.To gather further insights into interactive bioinformatics applications that are reusable, reproducible, accessible, and sustainable, this Research Topic will focus on application-layer solutions rather than purely computational methods without an end-user interface. We welcome articles addressing, but not limited to, the following themes:• Design and implementation of interactive bioinformatics applications, dashboards, packages, and analytical platforms• Transferable principles for converting bioinformatics analyses into usable and reproducible software• Comparative evaluation of frameworks, architectures, deployment models, and infrastructure• Usability, accessibility, user-centered design, and evaluation with research, clinical, laboratory, or public-health users• Software testing, input validation, error handling, performance, scalability, and maintainability• Provenance, audit trails, transparent parameters, reproducible reports, and workflow traceability• Open-source development, licensing, software citation, versioning, archiving, and dependency management• Deployment, containerization, workflow management systems, cloud infrastructure, security, monitoring, and stable citable services• Software sustainability, community governance, training, adoption, and long-term maintenance• Applications in genomics, transcriptomics, proteomics, metagenomics, clinical bioinformatics, structural biology, and related fieldsContributions should demonstrate value beyond a single local dataset or project through methodological novelty, reuse potential, rigorous evaluation, transferable design principles, or evidence of adoption and impact. Topic editors: Patricia Agudelo-Romero, Hugo López-Fernández Source: https://www.frontiersin.org/research-topics/86414/from-code-to-clicks-building-interactive-and-reproducible-bioinformatics-applications