--- vault_clearance: SAFE halo: classification: PUBLIC confidence: MEDIUM front: "05_Project_LENG — BOOK" custodian: "The Architect" created: 2026-03-30 updated: 2026-03-30 wing: READY containment: "BOOK — bibliography + methods registry; not README / WORLDLINE / BOUNTY" --- # LENG — BOOK Canonical bibliography and methods registry for **05_Project_LENG** (LOTUS / zero-parameter physics framework). 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). **Fusion note:** Drug / single-cell operator references below are migrated from [`HALO_AMBROSIA_DRUG_OPERATOR_MAP.md`](HALO_AMBROSIA_DRUG_OPERATOR_MAP.md) so this file stays the **canonical DOI index** for that thread; keep the HALO doc for narrative context. ### 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. Units, constants, and public software archive | ID | Kind | Note | Identifier | |----|------|------|------------| | L-B0 | Preprint / review | “Trialogue” on mass units and fundamental constants (cited in `public-release/README.md`) | [`arxiv.org/abs/physics/0110060`](https://arxiv.org/abs/physics/0110060) | | L-D1 | Dataset / software | LOTUS model archive (Zenodo) | [`10.5281/zenodo.18655472`](https://doi.org/10.5281/zenodo.18655472) | --- ## 2. Single-cell pharmacology and databases (from HALO Ambrosia map) | ID | Kind | Title / note | Identifier | |----|------|----------------|------------| | L-B1 | Primary | Massively multiplex chemical transcriptomics at single-cell resolution (*Science* 2020) | [`10.1126/science.aax6234`](https://doi.org/10.1126/science.aax6234) | | L-B2 | Primary | Multiplexed single-cell transcriptional response profiling (*Nat Commun* 2020) | [`10.1038/s41467-020-17440-w`](https://doi.org/10.1038/s41467-020-17440-w) | | L-B3 | Primary | Deconvolution of cell type-specific drug responses with scRNA-seq (*Genome Med* 2021) | [`10.1186/s13073-021-00894-y`](https://doi.org/10.1186/s13073-021-00894-y) | | L-B4 | Database | DrugBank 6.0 (*Nucleic Acids Res* 2024) | [`10.1093/nar/gkad976`](https://doi.org/10.1093/nar/gkad976) | | L-B5 | Clinical | Senolytics D+Q preliminary human report (*EBioMedicine* 2019) | [`10.1016/j.ebiom.2019.08.069`](https://doi.org/10.1016/j.ebiom.2019.08.069) | | L-B6 | Primary | PD-1 blockade persister cells (*JCI* 2020) | [`10.1172/JCI135038`](https://doi.org/10.1172/JCI135038) | | L-B7 | Methods | speedingCARs — CAR T engineering + scRNA-seq (*Nat Commun* 2022) | [`10.1038/s41467-022-34141-8`](https://doi.org/10.1038/s41467-022-34141-8) | --- ## 3. LOTUS build, theorems, and publication workflow (curate) | ID | Kind | Note | Identifier | |----|------|------|------------| | L-T1 | Repo | Canonical build | `lotus-universalis/build.py`, [`public-release/README.md`](public-release/README.md) | | L-B8 | Stub | arXiv / journal versions of the theorem paper — add DOIs when frozen | *See BOUNTY_BOARD* | --- ## 4. Bounty → start here | Workstream | Start with | |------------|------------| | Physics / LOTUS | [`README.md`](README.md), [`FORM.md`](FORM.md), `public-release/` | | Ambrosia / operators | §2, [`HALO_AMBROSIA_DRUG_OPERATOR_MAP.md`](HALO_AMBROSIA_DRUG_OPERATOR_MAP.md) | | Release | §1 (`zenodo`), [`public-release/README.md`](public-release/README.md) | --- ## STARS — US and international anchors **Constants, chemistry, and sequence archives** — complements §§1–2 (papers and DrugBank already US/EU-heavy). ### How to read STARS (context) **STARS** here are **numeric, chemical, and sequence infrastructure** hubs. They **ground physical and molecular claims**; **experimental** values still need primary literature. | ID | What this STAR denotes | Typical use in this BOOK | Not / caveats | |----|-------------------------|--------------------------|---------------| | L-S1 | NIST fundamental constants | **CODATA-style** constants for physics / chemistry | Check revision year; constants are periodically adjusted. | | L-S2 | BIPM SI Brochure | **SI unit definitions** | Authoritative for SI; not a lab protocol. | | L-S3 | PubChem | **Small-molecule** structures, IDs, properties | Curated vs computed fields differ; trace to PMID/DOI. | | L-S4 | DDBJ | **INSDC** sequence archive (Japan node) | Same logical archive family as SRA/ENA; IDs may cross-link. | | L-S5 | NCBI GEO + SRA | **Expression and read** discovery | **Accession ≠ biology** — read series SOFT for cell type and design. | | ID | Region | Kind | Note | Identifier | |----|--------|------|------|------------| | L-S1 | US | CODATA-style constants hub | NIST Fundamental Physical Constants | [nist.gov PML constants](https://www.nist.gov/pml/fundamental-physical-constants) | | L-S2 | Multilateral | SI brochure | BIPM | [bipm.org SI brochure](https://www.bipm.org/en/publications/si-brochure) | | L-S3 | US | Small-molecule data | PubChem (NIH) | [pubchem.ncbi.nlm.nih.gov](https://pubchem.ncbi.nlm.nih.gov/) | | L-S4 | Japan | INSDC partner archive | DNA Data Bank of Japan (DDBJ) | [ddbj.nig.ac.jp](https://www.ddbj.nig.ac.jp/) | | L-S5 | US | Expression / sequencing index | NCBI GEO + SRA | [GEO](https://www.ncbi.nlm.nih.gov/geo/) · [SRA](https://www.ncbi.nlm.nih.gov/sra) | ## 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 | |------|-----|---------| | DOI | `10.5281/zenodo.18655472}` | `public-release/README.md` | | GSE | `GSE139944` | `HALO_AMBROSIA_DRUG_OPERATOR_MAP.md` | --- *BOOK revision: 2026-04-01 — STARS context table.*