The validated scientific lineage that gives sporeGarden products their substance. Stand up the soil — data locations, provenance targets, domain thread maps — so that projectNUCLEUS can grow on top and products can focus on what matters to their audiences.
Organization: sporeGarden (products built on ecoPrimals) Generation: gen4 — composition and deployment License: AGPL-3.0-or-later (code), ORC (system mechanics), CC-BY-SA 4.0 (docs)
foundation is the scientific knowledge layer of the ecoPrimals ecosystem. It maps the complete validated lineage — 28 baseCamp companion papers, 8 springs with 13,100+ quantitative checks, 70+ reproduced papers, and 16 faculty and community contacts — as one unified whole, organized into 10 interconnected domain threads.
ecoPrimals (organisms) → syntheticChemistry (springs/validation) → sporeGarden (products)
↓ ↓
primalSpring projectNUCLEUS
(validates compositions) (deploys compositions)
↑
foundation
(the soil: what to validate,
where the data lives,
what the targets are)
projectNUCLEUS defines HOW to deploy (primals, graphs, gates). foundation defines WHAT to validate (data, papers, targets, threads). Products define WHO benefits (helixVision for biologists, esotericWebb for creators, blueFish for labs).
The foundation is the soil. NUCLEUS is the spore that grows on top. Products are the fruiting bodies.
The science is not separate. Anderson localization threads through microbial ecology, immunology, digester engineering, and plasma physics. The provenance trio validates game sessions, biological samples, and medical records using the same DAG/certificate/braid machinery. barraCuda's GPU math powers lattice QCD, protein structure prediction, environmental monitoring, and drug screening.
Separating these into independent foundations would sever the connections that make the ecosystem powerful. The foundation is one interconnected graph. Expression documents zoom into subgraphs.
| Thread | Domain | Key Springs | Key Contacts |
|---|---|---|---|
| 1 | Whole-Cell Modeling | hotSpring, wetSpring, healthSpring | ABG community |
| 2 | Plasma Physics / Lattice QCD | hotSpring | Murillo, Chuna, Bazavov |
| 3 | Immunology / Drug Discovery | wetSpring, airSpring, healthSpring | Gonzales, Lisabeth, Neubig |
| 4 | Environmental Genomics | wetSpring, airSpring | Anderson R., Cahill, Liao |
| 5 | Evolutionary Biology / LTEE | wetSpring, neuralSpring | Dolson, Waters |
| 6 | Agricultural Science | airSpring, groundSpring, wetSpring | Dong, Liao |
| 7 | Anderson Mathematics | hotSpring, groundSpring, wetSpring, neuralSpring | Kachkovskiy |
| 8 | Human Health / Clinical | healthSpring | Mok |
| 9 | Gaming / Creative | ludoSpring | — |
| 10 | Provenance / Economics | ludoSpring, primalSpring | — |
See lineage/THE_UNIFIED_LINEAGE.md for the complete mapping with
baseCamp paper numbers, spring check counts, and cross-thread connections.
Products are lenses — each pulls specific threads from the foundation and presents them for a particular audience.
| Product | Foundation Threads | Audience |
|---|---|---|
| helixVision | 1, 3, 4, 5 | Field biologists, wastewater engineers, lab scientists |
| blueFish | 4 + data pipeline across all threads | Labs needing sovereign ETL and format conversion |
| esotericWebb | 9 | Game designers, writers, solo creators |
| Patient Records | 8, 10 | Clinicians, patients |
| Games@Home | 9 | Players, citizen scientists |
# 1. Deploy NUCLEUS composition (via projectNUCLEUS)
cd ../../projectNUCLEUS/deploy
bash deploy.sh --composition nest --gate <active-gate>
# 2. Fetch public data sources and run validation with full provenance
cd ../../foundation/deploy
bash foundation_validate.sh --thread wcmThis fetches genomes from NCBI, proteomes from UniProt, pathway maps from KEGG — hashes everything with BLAKE3, registers artifacts in NestGate, executes validation workloads through toadStool, and commits the complete provenance chain (rhizoCrypt DAG + loamSpine ledger + sweetGrass braid).
See deploy/README.md for full options and the sediment layer model.
lineage/ The unified lineage — master map and thread index
THE_UNIFIED_LINEAGE.md Master document: 10 threads, all papers/springs/contacts
THREAD_INDEX.toml Machine-readable inventory for tooling
BASECAMP_PAPER_MAP.toml baseCamp papers → threads, springs, data anchors
expressions/ Domain thread expression documents
ABG_WHOLE_CELL_REBUILD.md Thread 1: whole-cell modeling (first expression)
data/ Data source manifests and validation targets
sources/ Per-thread data source TOMLs (10 threads, 150+ sources)
targets/ Per-thread validation target TOMLs (10 threads, 165+ targets)
graphs/ Foundation-specific deploy graphs (references projectNUCLEUS)
deploy/ Operational scripts
fetch_sources.sh Fetch NCBI/UniProt/KEGG data, compute BLAKE3 hashes
foundation_validate.sh Full validation pipeline with provenance wrapping
workloads/ toadStool-executable workload definitions per thread
specs/ Contracts and authoring guides
validation/ Validation results, provenance manifests, gap reports
handbacks/ Geological record from projectNUCLEUS deployment validation
COMPOSITION_GAPS.md Composition-level capability mismatches
docs/ External-facing primers and guides
BONDING_MODELS.md Atomic bonding architecture (covalent/ionic/metallic)
NUCLEUS_PRIMER.md Ecosystem primer — orientation for new contributors
| Repo | Org | Relationship |
|---|---|---|
| projectNUCLEUS | sporeGarden | The spore — deploys primals, produces gap handbacks that settle here as geological record |
| plasmidBin | ecoPrimals/infra | Binary depot — foundation validation runs use primals from here |
| primalSpring | syntheticChemistry | Composition validation — foundation references validated graphs |
| wateringHole | ecoPrimals/infra | Standards and guidance — foundation follows these |
| whitePaper | ecoPrimals/infra | Historical lineage — gen4/foundations/ is the personal record; this repo is the living expression |
| helixVision | sporeGarden | Product focus — pulls Threads 1, 3, 4, 5 from foundation |
| blueFish | sporeGarden (pending) | Product focus — pulls Thread 4 + data pipeline from foundation |
| esotericWebb | sporeGarden | Product focus — pulls Thread 9 from foundation |