overview of Pantheon-CLI, an advanced open-source computational framework developed by Stanford-affiliated scientist-engineers. It is presented as the initial release of PantheonOS, an "AgentOS that re-imagines Science," aiming to transform scientific research through an AI scientist paradigm. The core of Pantheon-CLI is its agent-driven, conversational workflow, which allows researchers to interact with data and perform complex, PhD-level analyses using mixed natural language and code. The system's modular architecture comprises three main components: pantheon-cli for the user interface, pantheon-agents as the reasoning core, and pantheon-toolsets for distributed execution, ensuring extensibility and adaptability across various scientific disciplines, particularly in data-intensive fields like genomics. The document also distinguishes Pantheon-CLI from other similarly named projects, highlights its support for local data processing and various LLMs, and identifies its primary audience as computational biologists and general data scientists.