Talk2Biomodels: AI agent-based open-source LLM initiative for kinetic biological models

Abstract

In this study, we present Talk2Biomodels (T2B), an open-source1, user-friendly, large language model-based agentic AI platform designed to democratize access to computational models of biological interactions and promote the FAIRification (Findability, Accessibility, Interoperability, and Reusability) of these models. T2B enables users to explore and analyse mathematical models of biological systems using natural language. It eschews the traditional graphical user interface (GUI) and minimally adaptable workflow in favour of a modern agentic framework to provide a dynamic and immersive experience to explore mathematical models of biological interactions through conversations in natural language. T2B supports models encoded in the open-source community format Systems Biology Markup Language (SBML) and is integrated with the BioModels database (https://www.ebi.ac.uk/biomodels/), enabling seamless exploration, simulation, and analysis of curated systems biology models. Use cases in precision medicine, epidemiology, and emergent systems properties of biological networks are presented to demonstrate how experts and non-experts in computational biology can benefit from T2B.