This paper introduces TOOLUNIVERSE, a comprehensive, open-source ecosystem designed to facilitate the creation of specialized AI scientists by integrating large language models and reasoning models with a vast array of scientific tools. This platform addresses the current difficulty of building bespoke AI research systems by standardizing tool interaction through an AI-tool interaction protocol and offering over 600 resources, including machine learning models, databases, and APIs. Key components such as the Tool Discover and Tool Optimizer enable the system to automatically generate new tools and refine existing tool specifications, going beyond simple tool orchestration. A case study on hypercholesterolemia demonstrates TOOLUNIVERSE's capacity to drive therapeutic discovery, moving from initial target identification to the validation of optimized drug candidates. Ultimately, the ecosystem aims to democratize the development of sophisticated AI research assistants and accelerate discovery across scientific domains.
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