hexa-bio — Molecular Toolkit (HEXA family)

4-verb molecular substrate organized around the n=6 invariant lattice: WEAVE / NANOBOT / RIBOZYME / VIROCAPSID. One sister axis (weave) is empirically wired with full Caspar-Klug + Zlotnick cage-assembly sandbox

• Bayesian σ(6)=12 STRUCTURAL-EXACT audit; three sister axes ship as stub placeholders with falsifier preregister at v1.0.0.

Status (2026-05-06): cycle 25 closed; v1.1.0 candidate drafted (see RELEASE_NOTES_v1.1.0.md). Cycle 25 traversed the 16-cell C2 matrix (4 verb × 4 disease class) at IN-SILICO grade — 16/16 cells PASS the simulator+metadata internal-consistency check. Honest caveat: C2 PASS verifies in-silico simulator+metadata internal consistency only — it is NOT therapeutic, clinical, regulatory, immunogenic, or efficacy progress. C3+ (wet-lab → IND → phase I) is explicitly out-of-repo. No medical claim is made or implied.

Distribution: GitHub canonical at https://github.com/need-singularity/hexa-bio. CLI tooling — installed via hx install hexa-bio from the hexa-lang registry, or git clone directly. (HF Hub mirror retired 2026-05-04: HF Hub is designed for ML model weights / datasets; CLI tooling distribution is GitHub-canonical.)

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What is hexa-bio?

hexa-bio is a standalone Molecular Toolkit that exposes 4 sister verbs for write-side molecular sandboxing. It is the empirical companion to n6-architecture/domains/biology/ and the canonical extraction-of-record for the WEAVE axis (cycle 24, 2026-04-29 → standalone 2026-05-04).

The 4 verbs form a tetrahedron organized around the n=6 invariant lattice:

                      ┌──────────────┐
                      │   composition│
                      │    (WEAVE)   │
                      └───────┬──────┘
                              │
              ┌───────────────┼───────────────┐
              │               │               │
   ┌──────────▼──────┐  ┌─────▼──────┐  ┌────▼────────┐
   │   actuation     │  │  catalysis │  │  assembly   │
   │   (NANOBOT)     │  │  (RIBOZYME)│  │ (VIROCAPSID)│
   └─────────────────┘  └────────────┘  └─────────────┘
       [STUB]              [STUB]            [STUB]

WEAVE is the only axis with full numerical empirical sandbox at v1.0.0 (T=1 60-subunit icosahedral cage; posterior 0.97). The other 3 axes ship as stub modules that print their falsifier preregister tables; their numerical implementations are deferred to post-v1.0 cycles.

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Installation

Via hx (recommended)

hx install hexa-bio          # global, pulls latest from registry
hx install hexa-bio@1.0.0    # pin specific version
hexa-bio --version           # → 1.0.0

hexa-bio is registered as the 24th entry in the hexa-lang package registry (hexa-lang/tool/pkg/registry.tsv L24). hx install hexa-bio pulls from https://github.com/need-singularity/hexa-bio and installs the standalone CLI under $HX_HOME/bin/hexa-bio.

Via git clone (works today)

git clone https://github.com/need-singularity/hexa-bio.git ~/.hexa-bio
export HEXA_BIO_ROOT=~/.hexa-bio
export PATH="$HEXA_BIO_ROOT/cli:$PATH"

# Run any subcommand:
hexa run $HEXA_BIO_ROOT/cli/hexa-bio.hexa selftest

Optional Python aux for weave's empirical-sandbox path

The default path needs zero Python deps (cached corpus result + pure-hexa skeleton). For weave's full cage-assembly ODE + live Bayesian audit:

pip install --user numpy scipy
export HEXA_BIO_WITH_NUMPY=1
hexa-bio weave --all

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Quick Start

1. Run the full self-test (4-verb sentinel sweep)

hexa-bio selftest

Output: __HEXA_BIO_SELFTEST__ PASS + per-verb sentinel lines (4/4 modules load + print falsifier tables). Sentinel-only PASS does not imply empirical claims validated (see Caveats §1).

2. WEAVE — protein cage / polyhedral self-assembly (WIRED)

hexa-bio weave                       # default skeleton (n=6 + falsifier table)
hexa-bio weave --bayesian-audit      # cached posterior 0.97 (no Python needed)

# Full empirical paths (requires HEXA_BIO_WITH_NUMPY=1):
HEXA_BIO_WITH_NUMPY=1 hexa-bio weave --cage-assembly --t-end 1000
HEXA_BIO_WITH_NUMPY=1 hexa-bio weave --bayesian-audit
HEXA_BIO_WITH_NUMPY=1 hexa-bio weave --all

3. NANOBOT — molecular actuation (STUB)

hexa-bio nanobot
# → prints n=6 lattice (hypothesized) + 3 falsifier preregister entries

4. RIBOZYME — RNA-catalyst (STUB)

hexa-bio ribozyme
# → prints n=6 lattice (hypothesized) + 3 falsifier preregister entries

5. VIROCAPSID — viral capsid assembly (STUB)

hexa-bio virocapsid
# → prints n=6 lattice (T=1 grounded via weave; T>1 hypothesized) + 3 falsifiers

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4-verb status table

Verb	Status	n=6 lattice verification	Empirical sandbox
weave	WIRED v1.0.0	STRUCTURAL-EXACT (T=1, post 0.97)	cage-assembly ODE + audit
nanobot	STUB v1.0.0-stub	hypothesized only	deferred (cycle 25+)
ribozyme	STUB v1.0.0-stub	hypothesized only	deferred (cycle 25+)
virocapsid	STUB v1.0.0-stub	partial (T=1 via weave)	deferred (T>1: cycle 25+)

Verdict: PARTIAL_PASS (1/4 verbs wired; 3/4 stubs with falsifier preregister).

For the full roadmap, see .roadmap.hexa_bio (repo-overall: lattice / gates / cycle 22 closure / deadlines) and the 4 per-verb sister files: .roadmap.weave · .roadmap.nanobot · .roadmap.ribozyme · .roadmap.virocapsid.

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16-cell C2 matrix (cycle 25, 2026-05-06)

Cycle 25 closed the C2 traversal of the 4 verb × 4 disease-class scaffold at IN-SILICO grade. Each cell ships a wrapper script in _python_bridge/module/*_candidate.py that records candidate-spec metadata annotated against publicly catalogued disease-class markers and verifies via the corresponding C0b simulator. Each cell emits one raw_77_c2_<verb>_<class>_v1 witness row to state/discovery_absorption/registry.jsonl.

Verb \ Class	α (AML)	β (SCD)	γ (pan-cov)	δ (senolytic)
W (weave)	PASS	PASS	PASS	PASS
N (nanobot)	PASS	PASS	PASS	PASS
R (ribozyme)	PASS	PASS	PASS	PASS
V (virocapsid)	PASS	PASS	PASS	PASS

Aggregate: 16/16 PASS (in-silico verification of simulator+metadata internal consistency only).

Honest caveat (raw#91 C3 discipline): a C2 cell PASS confirms only that (a) the C0b simulator runs deterministically, (b) the candidate-spec metadata schema validates, and (c) the verifier's internal consistency check holds. It does NOT imply any therapeutic, clinical, regulatory, immunogenic, pharmacokinetic, or efficacy property. The disease-class markers are publicly catalogued reference annotations — not medical claims. C3+ (wet-lab → in-vitro → in-vivo → IND → phase I) is explicitly out-of-repo per cross-cutting Require (R6).

Per-row witnesses are archived under design/kick/ (2026-05-06_hexa-{weave,nanobot,ribozyme,virocapsid}-c2-row-cycle25_omega_cycle.json) plus the aggregate 2026-05-06_hexa-bio-cycle25-c2-matrix-closure_omega_cycle.json.

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n=6 invariant lattice

The lattice anchors the toolkit to a single algebraic identity:

σ(6) = 12        STRUCTURAL-EXACT for T=1 cage (vertex count, posterior 0.97)
τ(6) = 4         4-state ladder (free / pentamer / hexamer / cage) — weave
φ(6) = 2         binary dichotomy (free vs assembled)
J₂   = 24        octahedral O ⊂ icosahedral I subgroup

master identity:   σ · φ = n · τ = 12 · 2 = 6 · 4 = 24

Per-verb interpretation (where empirically grounded vs hypothesized — see Caveats §3):

Symbol	weave (verified)	nanobot (hyp)	ribozyme (hyp)	virocapsid (partial)
σ(6)=12	cage vertex count	actuation cycle states	catalytic cycle states	T=1 cage (verified via weave)
τ(6)=4	4 ladder states	4 mechanical regimes	4 catalytic regimes	4 assembly stages
φ(6)=2	free vs assembled	bound vs unbound	bound vs free	assembled vs disassembled
J₂=24	I ⊃ O subgroup (geometric)	power-stroke trajectory	reaction-coordinate grp	I ⊃ O (T=1 exact; T>1 conjecture)

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Architecture

/Users/ghost/core/hexa-bio/
├── cli/
│   └── hexa-bio.hexa           # 4-verb router + status + selftest
├── weave/module/weave.hexa              # WIRED — Caspar-Klug + Zlotnick (cage 60)
├── nanobot/module/nanobot.hexa          # STUB — actuation primitive
├── ribozyme/module/ribozyme.hexa        # STUB — RNA catalyst primitive
├── virocapsid/module/virocapsid.hexa    # STUB — viral capsid assembly primitive
├── selftest/module/selftest.hexa        # 4-verb sentinel sweep
├── _python_bridge/module/
│   ├── cage_assembly_simulation.py        # weave ODE (numpy/scipy opt-in)
│   └── polyhedral_cage_bayesian_audit.py  # weave Bayesian audit
├── tests/
│   ├── test_weave.hexa
│   ├── test_nanobot.hexa
│   ├── test_ribozyme.hexa
│   ├── test_virocapsid.hexa
│   └── test_selftest.hexa
├── examples/
│   ├── 01_quick_weave.hexa
│   ├── 02_quick_nanobot.hexa
│   ├── 03_quick_ribozyme.hexa
│   └── 04_quick_virocapsid.hexa
├── design/kick/                # omega-cycle witness archive (cycle 24/25 closures,
│                               # schema `omega_cycle.witness_v1`)
├── install.hexa                # hx hook (pre/post)
├── hexa.toml                   # package manifest
├── LICENSE                     # Apache-2.0
├── CHANGELOG.md
└── README.md                   # (this file)

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Provenance

• WEAVE module imported from nexus/sim_bridge/weave/ (cycle 24 canonical, 2026-04-29). Original concept: n6-architecture/domains/ biology/hexa-weave/hexa-weave.md empirical companion.
• NANOBOT/RIBOZYME/VIROCAPSID modules created fresh as stub placeholders during this extraction (2026-05-04) — no prior nexus implementation existed beyond .roadmap / atlas.append marker entries (e.g. nexus/n6/atlas.append.hexa-nanobot-domain-registration.n6).
• Sister extractions:
  • qmirror v2.0.0 (registry L22, GitHub need-singularity/qmirror)
  • sim-universe v1.0.0 (registry L23, GitHub need-singularity/sim-universe)
  • hexa-bio v1.0.0 (registry L24) ← this repo

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Caveats (raw#10 honest C3)

1. 3/4 verbs are stub-only at v1.0.0. nanobot, ribozyme, and virocapsid ship as placeholders that print falsifier preregister tables and a sentinel — they do not run any numerical sandbox. The __HEXA_BIO_*__ PASS sentinels confirm only that the module loaded; they do not validate any empirical claim.
2. Falsifiers for stub verbs are initial-guess deadlines. Concrete experimental refutation criteria + dates were drafted during this extraction without literature corpus review for nanobot/ribozyme axes. Revision planned in cycle 25+.
3. n=6 invariant lattice claim is speculative for 3/4 axes. Only weave's σ(6)=12 (T=1 cage vertex count, posterior 0.97) is empirically grounded. The lattice mapping for nanobot's actuation cycles, ribozyme's catalytic cycles, and T>1 virocapsids is conjecture inherited from the lattice's algebraic structure, not from independent experimental fit.
4. Migration of nexus/sim_bridge/weave/ may break edge-case consumers. Cross-link consumers (n6-architecture papers, nexus/state/audit/cage_assembly_events.jsonl readers) reference the old path; the path-migration shim is left to the nexus consumer refactor cycle. The runs/ ledger (~10MB jsonl) is not vendored into this standalone repo by default.
5. GitHub-only distribution (HF Hub mirror retired 2026-05-04). HF Hub is designed for ML model weights / datasets, not CLI tooling. Maintenance burden (recurring token rotation failures) outweighed value. GitHub remains canonical at https://github.com/need-singularity/hexa-bio; HF Hub stays canonical for model weights / datasets in the wider stack.

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License

Apache-2.0. See LICENSE.

Optional Python aux deps (numpy, scipy) ship under their own BSD-3 licenses; in-process safe (no copyleft). hexa-bio core stays Apache-2.0 under FSF MereAggregation.

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Cross-links

• Sister standalone: qmirror v2.0.0 (quantum substrate — closure 13/13 conds, 8 v1 + 5 v2)
• Sister standalone: sim-universe v1.0.0 (simulation substrate)
• Sister standalone: honesty-monitor v1.0.0 (AI honesty-bit falsifier)
• Upstream concept SSOT: n6-architecture/domains/biology/hexa-weave/hexa-weave.md (declarative)
• Upstream formal SSOT: n6-architecture/lean4-n6/N6/MechVerif/
• Upstream paper SSOT: n6-architecture/papers/hexa-weave-formal-mechanical-w2-2026-04-28.md
• HEXA package registry: hexa-lang/tool/pkg/registry.tsv L24