BioMANIA: Simplifying bioinformatics data analysis through conversation

Abstract The burgeoning field of bioinformatics has been revolutionized by the rapid growth of omics data, providing insights into various biological processes. However, the complexity of bioinformatics tools and the rapidly evolving nature of data analysis pipelines present significant challenges for researchers, especially those lacking extensive programming expertise. To address these challenges, we introduce BioMANIA, an artificial intelligence-driven, natural language-oriented bioinformatics data analysis pipeline. BioMANIA comprises two key components: a ChatBot generation pipeline and a user-friendly ChatBot back-end service. The generation pipeline takes as input an open-source ( e.g ., hosted in GitHub) and well-documented ( e.g ., hosted in ReadTheDocs) Python tool, extracting API attributes and generating synthetic instructions that train a ChatBot to understand and perform specific data analysis tasks. We identified 11 common issues to provide a practical guideline for designing more ChatBot-compatible tools, which we categorized into five groups, while analyzing 12 well-documented open-source Python tools across various bioinformatics settings. The ChatBot service then assists users in selecting the appropriate analysis API and parameters, significantly reducing the programming barrier. We applied BioMANIA to analyze single-cell gene expression data, demonstrating its effectiveness in simplifying complex omics data analysis. BioMANIA has the potential to transform the landscape of bioinformatics research, making data analysis more accessible and accelerating discoveries in the field. 1