PantheonOS

PDF paper or tutorial—Pantheon-CLI reads it, plans steps, and replicates methods before analysis. 5. Task planning: Builds scientific agents by learning from papers/tutorials (not just fixed, human-predefined steps). 6. Multi-model support: Works with OpenAI, Anthropic, Gemini, DeepSeek, Qwen, etc. + offline local LLMs (ollama, deepseek, gpt-oss). 7. Multi-RAG support: Pre-learns from docs/web into a local “brain” for more credible outputs without massive token costs. 8. Built-in biology toolsets: For omics analysis (alignment, annotation, differential expression, full paper reproduction). 9. Notebook mode: Brings the same agentic workflow into Jupyter—automatically runs and revises code, operates on files, and learns from tutorials/papers. Pantheon-CLI is our attempt to push beyond “AI writes code for you.” Instead, it’s an agentic operating system for data analysis, spanning both terminal and notebook. Repo: https://github.com/aristoteleo/pantheon-cli Tutorial: https://pantheonos.stanford.edu/cli/docs/intro/getting-start... Home page: https://pantheonos.stanford.edu/ Would love to hear feedback from the HN community—what use cases would you try this for, and what features would make it more useful to you?

f evolving large-scale code projects to achieve superhuman performance (e.g., evolving upon the original Harmony [I Korsunsky, 2019, Nature Biotechnology] and Scanorama [BL Hie, 2019, Nature Biotechnology] implementations), and even evolving the system itself to adapt to new fields. Stepwise Release Strategy We’re releasing PantheonOS in stages: Pantheon-CLI (today!), followed by Pantheon-Lab, Pantheon-Notebook, Pantheon-Slack, and more. Pantheon-CLI Highlights - We're not just building another CLI tool. We're defining how scientists will interact with data in the AI era. - Open, Powerful, Python-First – The first fully open-source, endlessly extendable scientific “vibe analysis” framework. - Mixed Programming Magic – Combine Python, natural language, R, or Julia—seamlessly in the same environment. - PhD-Level Assistant – A command-line agent for complex real-world genomics and beyond, handling workflows at the PhD level. - Privacy by Design – Run entirely offline with local LLMs—your data never leaves your computer. Proven Applications (10 Demonstrations) Computational biology: 1. ATAC-seq: From raw reads to peak matrix 2. RNA-seq: From raw reads to expression matrix 3. Complex single-cell workflows (PhD-level) 4. Hybrid natural language + R for Seurat annotation 5. Learning from web tutorials + invoking single-cell foundation models 6. Cell segmentation on 10x Genomics HD Visium data And beyond: 7. Mixed Python & R programming examples 8. Molecular docking & structural analysis 9. Exploratory factor analysis for behavioral survey data 10. Customer segmentation & finance analytics Learn More & Get Started Website: http://pantheonOS.stanford.edu Pantheon-CLI Documentation: https://pantheon-cli-docs.netlify.app GitHub Repo: https://github.com/aristoteleo/pantheon-cli Join our community: PantheonOS Slack: https://pantheonos.slack.com/ssb/redirect PantheonOS Discord: https://discord.com/invite/74yzAGYW