---
vault_clearance: EUCLID
halo:
  classification: INTERNAL
  confidence: MEDIUM
  front: "08_Project_Astronomicon — BOOK"
  custodian: "Gemini"
  created: 2026-03-30
  updated: 2026-04-01
  wing: UNASSESSED
  containment: "BOOK — bibliography + methods registry; not README / WORLDLINE / BOUNTY"
---

# Project Astronomicon — BOOK

Canonical bibliography and methods registry for **08_Project_Astronomicon** (single-cell unified pipeline, warp / u-os edge). Convention: [`BOOK_Protocol.md`](../BOOK_Protocol.md). Orientation: [`README.md`](README.md). Open work: [`BOUNTY_BOARD.md`](BOUNTY_BOARD.md) · [`WORLDLINE.md`](WORLDLINE.md). Paradigm map: [`FORM.md`](FORM.md).

**Note:** No `doi.org` strings were found in canonical `08_Project_Astronomicon/*.md` at rollout time — add **published** method papers as each analysis path is frozen. Prefer DOI over vendor PDFs.


### Local registry slice (EYE / STAFF / STARS)

| Surface | Pointers |
|---------|----------|
| **EYEs** | Runs: [`README.md`](README.md) / [`WORLDLINE.md`](WORLDLINE.md) (if present). Registry: [`EYE_PROTOCOL.md`](../EYE_PROTOCOL.md) |
| **STAFF** | Runnable tools: [`STAFF_catalogue.json`](../STAFF_catalogue.json) — filter `project_dir` for this folder. |
| **STARS** | This file; rules: [`BOOK_Protocol.md`](../BOOK_Protocol.md). |
| **Audit sheet** | [`LOGGING_AND_REGISTRY_CHECKLIST.md`](../99_Archive/root_reports/2026-04/LOGGING_AND_REGISTRY_CHECKLIST.md) |


---

## 1. Core software stack (documentary links — verify versions in-repo)

| ID | Kind | Note | Identifier |
|----|------|------|------------|
| A-T1 | Software | Scanpy / Python single-cell stack | [https://scanpy.readthedocs.io/](https://scanpy.readthedocs.io/) |
| A-T2 | Software | Seurat (R) | [https://satijalab.org/seurat/](https://satijalab.org/seurat/) |
| A-T3 | Software | anndata / h5ad | [https://anndata.readthedocs.io/](https://anndata.readthedocs.io/) |
| A-T4 | Format | 10x Genomics file formats / support | [https://www.10xgenomics.com/support](https://www.10xgenomics.com/support) |

---

## 2. Downstream methods named in README (curate DOIs)

| ID | Kind | Note | Identifier |
|----|------|------|------------|
| A-B1 | Stub | CellChat, LIANA, decoupler, SCType, doublet callers — add **primary** citations when pipeline section cites them | *See README pipeline tables* |

---

## 3. u-os / deployment (curate)

| ID | Kind | Note | Identifier |
|----|------|------|------------|
| A-T5 | Internal | Worker / edge docs | [`u_os_dev/README.md`](u_os_dev/README.md) |
| A-T6 | Cloud | Scaleway Serverless Functions — EU-region edge/serverless compare bar | [https://www.scaleway.com/en/serverless-functions/](https://www.scaleway.com/en/serverless-functions/) |
| A-T7 | DNS | deSEC — EU-operated secure DNS hosting (DNSSEC) | [https://desec.io/](https://desec.io/) |

---

## 4. Bounty → start here

| Workstream | Start with |
|------------|------------|
| Pipeline | [`README.md`](README.md), [`FORM.md`](FORM.md) |
| Infra | §3 |

---

## STARS — US and international anchors

**Single-cell omics data** alongside §3 infra — NIH hubs plus EMBL-EBI / HCA.

### How to read STARS (context)

**STARS** here are **omics discovery and metadata portals**. They help you **find studies and reads**; **biology (cell type, treatment)** lives in each study’s GEO/SRA/BioSample metadata, not in the portal row itself.

| ID | What this STAR denotes | Typical use in this BOOK | Not / caveats |
|----|-------------------------|--------------------------|---------------|
| A-S1 | NCBI GEO | **Expression / microarray / series** landing pages | Always open the **GSE/GSM** SOFT or supplement for design. |
| A-S2 | NCBI SRA | **Raw read** archive | Run-level ≠ biological replicate — use BioSample grouping. |
| A-S3 | BioStudies | **Study metadata** (ArrayExpress lineage) | Cross-walk IDs to GEO when both exist. |
| A-S4 | HCA Data Portal | **Human** atlas collections | Consent and schema vary by project; read project cards. |
| A-S5 | PubMed | **Literature** index | Linkout to PMC/DOI; still read methods sections. |

| ID | Region | Kind | Note | Identifier |
|----|--------|------|------|------------|
| A-S1 | US | Gene Expression Omnibus | NCBI GEO | [ncbi.nlm.nih.gov/geo](https://www.ncbi.nlm.nih.gov/geo/) |
| A-S2 | US | Sequence Read Archive | NCBI SRA | [ncbi.nlm.nih.gov/sra](https://www.ncbi.nlm.nih.gov/sra) |
| A-S3 | UK / EU | Study metadata / expression | BioStudies (incl. ArrayExpress migration) | [ebi.ac.uk/biostudies](https://www.ebi.ac.uk/biostudies/) |
| A-S4 | International | Human Cell Atlas data | HCA Data Portal | [data.humancellatlas.org](https://data.humancellatlas.org/) |
| A-S5 | US | Biomedical literature | PubMed | [pubmed.ncbi.nlm.nih.gov](https://pubmed.ncbi.nlm.nih.gov/) |
<!-- accession_scan:generated -->

## Accession gap index (automated scan)

**Generated:** 2026-03-30. **Policy:** Mentions found under this project (excluding `_archive/`, `u_os_dev/out/public_lab/`, `.git/`, `node_modules/`) outside root `BOOK.md`, that do **not** appear as a substring anywhere in **this** `BOOK.md` yet. **Curated sections above remain authoritative** — merge rows into them when ready.

| Kind | ID | Seen in |
|------|-----|---------|
| GSE | `GSE160672` | `u_os_dev/CLAUDE_BOUNTY_HANDOFF.md` |

<!-- /accession_scan -->

---

*BOOK revision: 2026-04-01 — STARS context table.*