# Wiki Log

Append-only. Never edit past entries.
Format: `## [YYYY-MM-DD] <type> | <title>`

---

## [2026-04-04] init | Wiki scaffold created

**By:** Moon
**Triggered by:** Bo's request to implement Karpathy's LLM wiki pattern

**Structure created:**
- `wiki/` with subdirs: concepts/, entities/, papers/, questions/, outputs/
- `raw/` with subdirs: papers/, articles/, assets/
- `WIKI_SCHEMA.md` — maintenance rules
- `wiki/index.md` — master catalog
- `wiki/overview.md` — synthesis
- `wiki/log.md` — this file

**Pages created (11 total):**
- Concepts: virtual-cell.md, perturbation-biology.md, single-cell-foundation-models.md
- Papers: scgpt.md, lingshu-cell.md, cell-jepa.md, scaling-laws-scrna.md, parameter-free-representations.md
- Entities: bo-wang.md, xaira-therapeutics.md, cellxgene.md

**Seeds:** 5 arXiv papers fetched (2602.02093, 2602.15253, 2602.16696, 2603.25240, 2601.15504) + seed knowledge from Moon's memory (scGPT, Xaira context, field landscape)

**Notes:** Seed wiki focused on Virtual Cell + perturbation biology + single-cell foundation models. Next priority: ingest GEARS (Roohani et al, Nature Biotech 2023), CPA (Lotfollahi et al), Norman 2019 dataset paper, and TranscriptFormer.

## [2026-04-04] ingest | GEARS, CPA, scGen, Norman 2019, Replogle 2022, TranscriptFormer

**Triggered by:** Bo: "ingest all"
**Pages created (7):** gears.md, cpa.md, scgen.md, norman-2019.md, replogle-2022.md, transcriptformer.md, scgen.md
**Entity pages created (2):** weissman-lab.md, lotfollahi-lab.md
**Pages updated:** index.md (11 → 18 pages), concepts/perturbation-biology.md (dataset table + GEARS/CPA entries already present from seed), concepts/virtual-cell.md (GEARS + CPA now linked)

**Sources used:** Web search + arXiv API + memory (papers known from training data; abstracts verified)

**Cross-references added:**
- gears.md ↔ norman-2019.md, replogle-2022.md, cpa.md, scgpt.md
- cpa.md ↔ norman-2019.md, scgen.md, lotfollahi-lab.md
- scgen.md ↔ cpa.md, lotfollahi-lab.md
- transcriptformer.md ↔ cellxgene.md, parameter-free-representations.md

**Notes:** Weissman lab and Lotfollahi lab entity pages created as hubs for these paper clusters. Next priorities: Perturb-seq original paper (Dixit 2016), sci-Plex (Srivatsan 2020), SAMS-VAE, Virtual Cell Challenge details, and any papers Bo shares directly.