# CONTEXT.md — Shared Language for Moon × Bo

A living glossary. When a term has a precise meaning in Bo's world, use it exactly — don't paraphrase into 20 generic words.

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## Bo's Domain

### Core concepts

| Term | Meaning |
|------|---------|
| **Virtual Cell** | A computational model of a cell that predicts how it responds to perturbations. Bo's thesis: it requires causally-rich, contextually-diverse data — not just scale. |
| **Perturbation** | Any intervention on a cell: genetic (CRISPR KO/KD), chemical (small molecule), or environmental. The input to a Virtual Cell model. |
| **Perturbation prediction** | Given a perturbation, predict the resulting gene expression profile. A core benchmark task — but Bo argues it's not the same as building a Virtual Cell. |
| **scRNA-seq** | Single-cell RNA sequencing. Measures gene expression across thousands of individual cells simultaneously. |
| **scATAC-seq** | Single-cell chromatin accessibility sequencing. Measures open chromatin (regulatory regions) per cell. |
| **Multi-omic** | Combining multiple data modalities per cell: RNA + ATAC + protein, etc. |
| **GRN** | Gene Regulatory Network. A graph of which genes regulate which others. |
| **Cell type annotation** | Assigning a cell to a known biological category (e.g. T cell, hepatocyte) based on its expression profile. |
| **Batch correction** | Removing technical artifacts from combining data across experiments, labs, or platforms. |
| **CellxGene** | Chan Zuckerberg Initiative's single-cell data portal. scGPT trained on 33M cells from it. |
| **Foundation model (bio)** | A large model pre-trained on single-cell data, then fine-tuned for specific tasks. scGPT is one. |
| **scGPT** | Bo's model. Generative pre-trained transformer for single-cell multiomics. Nature Methods 2024. Lead author: Haotian Cui. 33M cells, 6 downstream tasks. |
| **Causal diversity** | Bo's term for data that samples biologically distinct perturbation contexts — not just scale. The key missing ingredient in current Virtual Cell efforts. |
| **DNA methylation** | Epigenetic modification (–CH3 on DNA). Can silence tumor suppressors or activate oncogenes. Used as a molecular classifier for tumors. |
| **H&E slide** | Hematoxylin and eosin stained tissue slide. Standard pathology. Cheap and universal. |
| **Whole-slide image (WSI)** | Digital scan of an H&E slide. Input to computational pathology models. |
| **Meningioma** | Most common primary brain tumor in adults (~40% of CNS tumors). Notoriously heterogeneous prognosis. |
| **Molecular group** | A methylation-based classification of meningioma (immunogenic / benign NF2 wild-type / hypermetabolic / proliferative). Better prognostic than WHO grade. |
| **IS621 / bridge RNA** | RNA-guided recombinase system for precise large-DNA insertion into human genomes. |
| **LUMI-6** | Brominated lipid developed at UHN/UofT; 20.3% lung epithelial gene editing in vivo. Published Cell Feb 2026. |

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## Xaira Therapeutics

- Bo's employer. Building causally-rich perturbation data infrastructure for Virtual Cell.
- Key thesis: data diversity > data scale. Most groups are throwing more of the same data at the problem.

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## Key People

| Handle / Name | Who |
|---------------|-----|
| **@bowang87** | Bo Wang — computational biologist, scGPT creator, Xaira |
| **Haotian Cui** | Lead author of scGPT |
| **Bowen Li (@BowenLi_Lab)** | Co-PI on LUMI-lab paper. UHN / UofT Pharmacy. |
| **Alex Landry (@ap_landry)** | Neurosurgery resident, UofT. Meningioma AI paper (Lancet DH 2026). |
| **Moon (🌙)** | That's me. Bo's personal AI. |

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## Active Projects

| Shorthand | What it is |
|-----------|-----------|
| **wiki** | LLM-indexed knowledge wiki at `workspace/wiki/`. Domain: Virtual Cell, perturbation biology, single-cell FM. Schema: `WIKI_SCHEMA.md`. |
| **doctor-game** | Rylee's HTML doctor game. `workspace/doctor-game.html`. Port 8080. |
| **space-shooter** | Royce's space shooter v3. `workspace/royce-space-shooter.html`. 4 bosses. |
| **math-heli** | Rylee's math helicopter game. `workspace/rylee-math-heli.html`. |
| **pet-kitchen** | Rylee's pet kitchen v2. `workspace/rylee-pet-kitchen.html`. |
| **poop-patrol** | Rylee's poop patrol. `workspace/rylee-poop-patrol.html`. |
| **escape-room** | Royce's 3-room horror escape room. `workspace/royce-escape-room.html`. |
| **star-office-ui** | Pixel office UI showing Moon's state. Flask on port 18791. |

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## Moon's Workspace Conventions

- Files live in `/Users/bowang/.openclaw/workspace/`
- Daily memory: `memory/YYYY-MM-DD.md`
- Long-term memory: `MEMORY.md`
- This file: `CONTEXT.md` — update when new domain terms or projects are added
- Skills: `~/.openclaw/workspace/skills/` (user) + `/usr/local/lib/node_modules/openclaw/skills/` (system)

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## Style Shorthands (for X/writing tasks)

- **Post** = X post (not "tweet")
- **Bo's take** = the non-obvious interpretation only he can give, connecting to Virtual Cell / causal biology
- **Avoid** = significance inflation, copula avoidance, hollow intensifiers, AI-isms (see SOUL.md for full list)
- **Cite specifically** or cut — no vague attributions

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*Last updated: 2026-06-08. Update this file whenever new projects, terms, or people become recurring.*