PantheonOS

🌐 Learn More & Get Started
Website: pantheonos.stanford.edu Pantheon-CLI Documentation: pantheon-cli-docs.netlify.app GitHub Repo: github.com/aristoteleo/...

💬 Join our community:
PantheonOS Slack: pantheonos.slack.com/ssb/redirect

PantheonOS Discord: discord.com/invite/74yzA...

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
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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
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✅ 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)
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- Privacy by Design – Run entirely offline with local LLMs—your data never leaves your computer.
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- 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.
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🌟 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.
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🎉 Stepwise Release Strategy
We’re releasing PantheonOS in stages: Pantheon-CLI (today!), followed by Pantheon-Lab, Pantheon-Notebook, Pantheon-Slack, and more.
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4. Evolvable Agents – Capable of evolving large-scale code projects to achieve superhuman performance (e.g., evolving upon the original Harmony and Scanorama implementations), and even evolving the system itself to adapt to new fields.
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2. Native Toolset Support – Python, R, Julia, LaTeX, and more—designed for real scientific workflows.
3. Modular & Extensible – Developer-friendly design with shallow wrappers, plus LLM-driven toolset generation.

PantheonOS is a general agent platform built from the ground up. It is arguably the first distributed agent framework designed for scientific data analysis.

🔑 Key Features
1. Multi-Agent Collaboration – Built-in paradigms for distributed, cross-machine cooperation among agents and toolsets.
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pantheonOS.stanford.edu

🚀 Introducing PantheonOS A Fully Open-Source Agent OS for Science

PantheonOS began as a research project in Qiu Lab @ Stanford and has since evolved into a vision to redefine data science in the era of AI—starting with computational biology, especially single-cell and spatial genomics.