ASTRA-Unified-ResearchLab-MCP-FCS-v3.1.0

ASTRA — Unified Research Lab + MCP Server

Agent-orchestrated Simulation Testbed for Research on Awareness

Data provenance. All biological and physiological data produced by this server are simulated. No living tissue, organoid, human subject or Koniku hardware is connected: the NeuroPlatform bridge is instantiated in simulate mode, the OVOMIND live adapter is an unimplemented stub, and the sensory encoders are untrained re-implementations inspired by V-JEPA 2 / A-JEPA. The consciousness-related indices are computed proxies, not measurements, and ASTRA makes no claim of sentience (the acronym's former expansion, Autonomous Sentient Thoughtful Reasoning Agent, is withdrawn — see src/engine/tcai/phenomenal-guard.ts).

First empirical test (E1). The organoid surrogate's spontaneous activity was confronted with three real human brain organoids (DANDI 001603) under a preregistration made public before the data were received. Verdict: INADEQUATE — the real organoids burst and synchronise, the surrogate emits independent Poisson trains; the failure is structural, not parametric. Protocol, results and replay: empirical/.

Second test (E2, preregistered). A candidate revision (spontaneousModel: 'network-burst': shared network bursts + locally clustered background, 9 parameters calibrated on the three E1 organoids only) was frozen, made public, then confronted with five unseen organoids (sub-HO1…HO5), with the E1 model as negative control. Verdict: PARTIALLY ADEQUATE (0 incompatible, 2 compatible, 3 marginal; the a-priori prediction "adequate" is refuted; the control stays INADEQUATE). The structural E1 failure is fixed, but the calibration does not transfer across organoids, notably to older (7-month) ones. The default model stays 'poisson'. empirical/RESULTS-E2.md.

Production-grade Model Context Protocol server exposing the ASTRA bio-hybrid neuromorphic simulation pipeline to AI assistants. Built with the official @modelcontextprotocol/sdk, it integrates a layered SNN LIF+STDP engine, consciousness proxy assessment, bio-computing platform telemetry, and an IRB ethics monitor — all queryable as MCP tools, resources, and prompts from Claude Desktop, Cursor, VS Code, and any MCP-compatible client.

🆕 v3.1.1 — Coherence corrections (audit of 6 October 2026)

Five corrections from a critical audit of v3.1.0. Each one fixes a point where the server contradicted its own FCS series or its own empirical results.

1. Calcium is no longer bound to class 1. ASTRA's eth.ca is intracellular free Ca²⁺ in nM (ethics.ts): the second messenger, which document IV §2 and synthesis S-1.6 place outside class 1. v3.1.0 bound it to class 1 as "extracellular Ca²⁺ at the MEA bath", a category error, and one of scale too: bath Ca²⁺ is about 1–2 mM. Class 1 now reads only an extracellular value in mM (extracellularCalciumMm, supplied by the caller), and is withheld() otherwise. eth.ca is reported and bound to no pair.

2. No consciousness scale anywhere; every payload is screened. get_acm_score binned its weighted composite into six labels, ABSENT…FULL. That is a quantified degree of consciousness (prohibition 1) built from an aggregate (prohibition 4). The labels and decisionClass are removed. The composite remains, but only as a declared engineering index (aggregationStatus).

   • New src/lint-guard.ts. Every tool and resource payload passes lintClaim and lintFcs; v3.1.0 screened only 20 of 70 tools. fcs_lint is exempt because it echoes the text it screens.
   • Linter fixes. The P3 rule's ungrouped alternation fired on any sentence containing "mécanisme". A year in parentheses no longer exempts an assertion, and naming a prohibition no longer exempts a sentence that asserts a value. Common paraphrases are now caught ("consciousness level 0.7", "71 % conscious", "Phi equals phenomenal experience"). An ordinal unit label no longer makes two ranks commensurable under P4.

3. The τ ordinalisation is published, and the strata are put in their place.

   • Document IV v1.3. FCS v1.5/Implementation Neurochimique FCS v1.3.html §2 declares the reduction that links the τ ranges to the strata. Matching the published strata checks the transcription; it does not validate the cuts. Of ten plausible reductions, only the declared one reproduces the strata (ordinalisationSensitivity()).
   • The dominance relation itself. fcs_stratify now returns 93 comparable pairs out of 136 and the Hasse diagram.
   • What strata do not order. 28 of the 121 cross-stratum pairs are incomparable.
   • Context dependence. Removing the ion shifts the other sixteen pairs, so a stratum is a label of the peeling, not a property of the pair. fcs_compare says so when two incomparable pairs sit in different strata.

4. Welfare thresholds recalibrated on DANDI 001603. The firing-rate range was 15–45 Hz, with ≤ 5 Hz critical. Every real organoid confronted in E1/E2 (median per-unit rate 0.14–0.62 Hz) would have been reported in distress. eth.fr is now the median per-unit rate:

   • normal 0.14–0.63 Hz (observed range of the eight organoids);
   • stress within a factor 2 of that range;
   • distress beyond.

   This is a descriptive reference interval from one dataset, not a validated welfare criterion.

5. Aligned on synthesis S-1.6, counts and licensing corrected.

   • S-1.6 belt extension. src/engine/fcs/optogenetics.ts encodes:

     • what each intervention dissociates, with a check that no intervention both breaks the generative dependence and satisfies the P5 clause;
     • the astrocytic anchoring, decomposed onto pairs already in the table;
     • a candidate astrocytic pair that is equivalent to class 8 and adds no distinction.

     fcs_report and astra://fcs/framework carry this extension.

   • Counts. References updated to IV v1.3 and S-1.6.

   • Licensing. package.json declares MIT AND LicenseRef-TCAI-NonCommercial and ships THIRD_PARTY_NOTICES.md and the upstream licence. CITATION.cff points to the licensing statement instead of declaring MIT for the whole.

   • Dependencies. npm audit fix brings vulnerabilities back to 0.

Test suite 331 → 354 tests · 66 suites (tests/lint-guard.test.ts added; FCS 69 → 86). Not addressed here and still open:

• the organoid realisation verdicts for myelin (11) and genomic hormones (9a), which the culture protocol should decide;
• the read-only annotation of get_acm_score, whose assess() updates acm.*;
• the M2 asymmetry in withdrawal.ts.

---

v3.1.0 — FCS layer: substrate-constrained functionalism

Implements the values of the FCS series (documents I v1.5, II v1.4, IV v1.3 — table as in v1.2 —, synthesis S-1.6) inside ASTRA as fcs_* tools — not as a scoring module.

• The stratification is computed, never hard-coded. The seventeen species–function pairs are ordered by Pareto dominance over three ordinal sub-criteria (causal distance to the carrier, time constant, ablation effect), peeled into a partial order. tests/fcs.test.ts asserts that the result reproduces the eight strata published in document IV §3 exactly — the only way to know the transcription is right.
• No aggregate score exists, anywhere in the layer. The series' negative heuristic forbids aggregating ordinal criteria lacking a common scale (prohibition 4, after Okasha 2011). mayAggregate() refuses such a combination at runtime; refuseAggregate() returns a withheld scalar carrying its reason instead of a number.
• The IRB welfare biomarkers are bound to the taxonomy. ATP/ADP is class 7, firing rate is the class-3 generator signature, viability stands proxy for class 2b. (v3.1.0 also bound eth.ca to class 1; corrected in v3.1.1 — see above.) A drifting biomarker becomes a statement about which pair has left its operating range. A silent channel yields withheld(), never zero.
• The silicon SNN realises no constitutive pair, and the audit says so: under the substrate constraint the level-I carrier is absent there, whatever the level-III/IV profile shows.
• Two linters gate every payload — lintClaim (Block's access/phenomenal distinction) and lintFcs (the five prohibitions), the latter distinguishing use from mention so that stating a prohibition or citing a title does not fire it. (In v3.1.0, the FCS, Orch OR and OVOMIND families only; server-wide since v3.1.1.)
• MCP surface: 62 → 70 tools (fcs_* ×8); resources 11 → 15, prompts 8 → 10. Test suite 241 → 317 tests (69 in tests/fcs.test.ts, 7 in tests/annotations.test.ts).
• MCP tool annotations on all 70 tools (title + read-only / destructive / idempotent / open-world hints), classified from each handler's code — see MCP Tools.
• Corrections before dissemination. Acronym re-expanded without "Sentient"; data provenance stated up front; encoder labels now read "…-inspired (untrained)"; get_acm_score retitled as a composite proxy; every stochastic component draws from one seeded generator (ASTRA_SEED, reported by get_system_status, export_snapshot and /health); third-party article copies replaced by a DOI bibliography; THIRD_PARTY_NOTICES.md, CITATION.cff, PREREGISTRATION.md and REVIEW.md added. Test suite 323 tests (6 in tests/reproducibility.test.ts).
• Dependencies hardened. express 4 → 5 (the MCP SDK already ran on Express 5; the project's @types/express were already v5) and tsx → 4.23 (bundles a patched esbuild): npm audit reports 0 vulnerabilities (previously 11, of which 7 in runtime dependencies). No code change was needed; the 12 transport tests pass unchanged.
• New console: dashboard/ASTRA-FCS-Dashboard.html — self-contained, bilingual FR/EN, recomputing the partial order in the browser and reporting whether it reproduces the published strata.

→ FCS-INTEGRATION.en.md · FCS-INTEGRATION.fr.md

---

🆕 v3.0.1 — Transport-layer audit: blocking fix + integration suite

A code audit of the v3.0 tree found that both HTTP transports were inoperative at runtime despite a fully green test suite. express.json() consumes the request stream, and the MCP SDK requires the already-parsed body to be handed back (handleRequest(req, res, req.body) / handlePostMessage(req, res, req.body)); without it the SDK re-read an empty stream and every client→server POST hung until timeout. The 229 tests never exercised the transports, so the defect survived them.

• Fix: parsed body forwarded at all four call sites (http-server.ts ×3, sse-server.ts ×1). Verified end-to-end: initialize → tools/list (62) → DELETE.
• Session-leak guard: a POST without a session that is not a valid initialize now returns a JSON-RPC -32000 (HTTP 400) instead of silently constructing an orphaned server instance.
• Version unified: src/version.ts is the single source of truth. The MCP server previously announced 2.2.0 to clients, while /health reported 2.0.0 (SSE) and 2.9.0 (HTTP).
• Bind address: both transports default to 127.0.0.1; containers set 0.0.0.0 explicitly. See Environment Variables.
• Lint restored: ESLint ≥ 9 requires a flat config, which the repo lacked — npm run lint failed outright and CI tolerated it via continue-on-error. eslint.config.js is now wired and lint is a blocking CI gate.
• New suite: tests/transports.test.ts — 12 integration tests over both HTTP transports (session lifecycle, tool-count contract, CORS preflight, guards, and named regression tests under a hard timeout so a re-introduced hang fails loudly rather than freezing the run). Total: 241 tests.

Testability required a small refactor: createHttpApp() and createSseApp() are now exported factories bound to ephemeral ports by the tests, while an import.meta.url entry-point guard preserves direct node dist/*-server.js execution.

🆕 v3.0 — Unified release: OVOMIND bridge + Orch OR criterion layer + CI fix

v3.0 = the full v2.9 core (unchanged) plus the affective exteroception bridge and the Orch OR substrate-criterion layer, wired and passing:

• src/engine/ovomind.ts — OVOMIND adapter (sim by default; the live adapter is a deliberate stub pending a vendor API contract), Russell→PAD lift (dominance is never estimated from peripheral physiology), gated closed-loop controller (ships disarmed; refuses to arm without a protocol reference).
• src/engine/tcai/phenomenal-guard.ts — epistemic tiers (access/functional only — no constructor for a phenomenal claim), Argonov ledger, Metzinger gate, claim linter. All 12 new tools route their output through it.
• src/engine/tcai/orch-or.ts — Penrose criterion τ=ℏ/E_G with the displacement scale exposed as the free parameter it is, decoherence budget (verdict: UNRESOLVED), per-substrate verdicts, and a classical surrogate gate (temporal signature only — explicitly NOT an implementation of Orch OR).
• MCP surface: 50 → 62 tools (ovo_* ×6, orch_* ×6); resources and prompts unchanged (11 · 8). The stdio smoke test asserts the new count.

Docs: OVOMIND-INTEGRATION.md (FR) · ORCH-OR-INTEGRATION.fr.md / .en.md.

CI fix shipped in this release. The previous lockfile pinned safe-stable-stringify@2.9.0 — a version that does not exist on the npm registry (both matrix jobs failed at npm ci with E404 in ~17 s). The lockfile now pins 2.5.0, which satisfies pino's ^2.3.1. ci.yml also gains the Python + numpy setup that golden:check silently required, bumps actions to v5 (ends the Node 20 deprecation warnings), and updates the tool-count assertion to 62.

Note: the separate ASTRA-3.0- repository (CL1 ↔ Unreal Engine UDP bridge, Python) is a companion system, not a version of this MCP server, and is not merged here.

🆕 v2.9 — Setpoint regulation + real production loop

ASTRA v2.9 makes the continuous controller non-degenerate: instead of ramping the substrate to maximum, it regulates toward a configurable setpoint (homeostatic drive cost ⇒ interior optimum; the realised feature tracks the setpoint). The closed loop can now run through the shared production SNN (read + write) via setProductionLoop, genuinely closing on the deployed network — off by default to avoid contention with snn_step. The two active-inference roles are made explicit (discrete core = perception/F; continuous controller = control), with controllerSetpoint/controllerModelError surfaced in telemetry and setpoint/productionLoop exposed on tcai_cycle. Still a linear forward model over a synthetic SNN-firing proxy. See SECOND-ORDER-LOOP-INTEGRATION.md.

🆕 v2.2 — the_consciousness_ai (ACM) Integration

ASTRA v2.2 integrates tlcdv/the_consciousness_ai — the Artificial Consciousness Module research codebase — at two levels:

• Native TypeScript port (src/engine/tcai/): Global Neuronal Workspace with sigmoid ignition & reverberation, Kuramoto/AKOrN oscillatory binding, PAD emotional processing & reward shaping, attention-gated emotional memory, self-representation core + attention schema, and a metrics suite (GNW · Effective Information · Φ̃-RIIU) — all fed live from the SNN/world-model state and exposed as 8 new MCP tools (tcai_cycle, tcai_workspace_state, tcai_emotion_appraise, tcai_memory_store, tcai_memory_retrieve, tcai_self_model, tcai_metrics, tcai_reset).
• Full vendored Python codebase (python/the_consciousness_ai/, 291 files — distributed under its own non-commercial licence, see License and THIRD_PARTY_NOTICES.md): the complete upstream ACM project for reference and PyTorch-based reproduction.

See TCAI-INTEGRATION.md for the complete Python → TypeScript mapping and architecture coupling. All consciousness-related metrics remain computational proxies, not measurements.

🆕 v2.2 — FinalSpark NeuroPlatform v2 Integration

ASTRA v2.2 also integrates the FinalSpark NeuroPlatform v2 wetware control API — the closed-loop interface to living neural organoids on a 128-electrode MEA — at two levels:

• Native TypeScript port + integration-test surrogate (src/engine/neuroplatform.ts): faithful port of the NeuroPlatform controller surface (StimParam with charge-balance checking, IntanController, TriggerController, DatabaseController, CameraController) backed by a seeded OrganoidMEA model — exposed as 9 new MCP tools (np_status, np_configure_stim, np_send_trigger, np_count_spikes, np_query_spike_count, np_query_spike_events, np_query_triggers, np_camera_capture, np_closed_loop). The MEA's 128 electrodes couple one-to-one with the ASTRA SNN's 128 neurons.
• Live Python bridge (python/neuroplatform/astra_np_bridge.py): runs a homeostatic closed loop against the physical platform via the genuine neuroplatformv2 SDK, streaming couplings to ASTRA over JSON-RPC.
• Standalone dashboard (dashboard/ASTRA-NeuroPlatform-Dashboard.html): live MEA raster, spike scope, StimParam editor with charge-balance readout, trigger generator and closed-loop telemetry.

See NEUROPLATFORM-INTEGRATION.md for the complete API → TypeScript mapping. With no hardware attached the server runs in simulate mode (deterministic Poisson surrogate), not living-tissue measurements. The surrogate's spontaneous activity was confronted with real human brain organoids (DANDI 001603) under a public preregistration and found inadequate (no network bursts, no synchrony) — see empirical/RESULTS-E1.md.

FinalSpark (800K neurons) ──┐
Cortical Labs CL1 ──────────┼─→ Spike Encoders → SNN (LIF+STDP, 128 neurons) → ACM Proxies
Koniku Kore ────────────────┘         │                    │
                                      │              ┌─────┴─────┐
                                      │              │  Φ̃  GW̃  PAD̃  │
                                      │              └─────┬─────┘
                                      ├─→ TCAI/ACM Layer (GNW · AKOrN · PAD · Φ̃-RIIU · EI)
                                      ├─→ NeuroPlatform v2 Bridge (MEA ↔ SNN · StimParam · closed loop)
                                      ├─→ Ethics IRB Monitor (mode-aware)
                                      └─→ MCP Server (70 tools · 15 resources · 10 prompts)

Note on data mode: In the default sim mode, all bio-platform data is synthetically generated. The server is designed to connect to live platforms in live mode, but this requires hardware access and appropriate IRB approval.

---

What's New in v2

• Layered SNN architecture: Configurable feed-forward + recurrent topology (default: 32→64→16→16 = 128 neurons) replacing the flat random network
• Event-driven STDP: O(spikes × fan-out) instead of O(N²) per timestep
• Ring buffer: O(1) spike history eviction replacing O(n) Array.shift()
• Sparse weight storage: Adjacency lists instead of dense N×N matrix
• Honest ACM naming: Proxies clearly labelled as integrationProxy, broadcastProxy, arousalProxy with methodological basis strings — no false IIT/GWT/PAD claims
• Bounds-checked parameters: set_parameter rejects implausible values (NaN, Infinity, out-of-range)
• Mode-aware ethics: Reports distinguish simulated vs live data with explicit disclaimers
• CI pipeline: GitHub Actions for build, test, and Docker smoke-test
• Repo hygiene: dist/ excluded from VCS, .gitignore added, deployment script removed

---

Quick Start

git clone https://github.com/christophejlegros-lgtm/ASTRA-Unified-ResearchLab-MCP-FCS-v3.1.0.git
cd ASTRA-Unified-ResearchLab-MCP-FCS-v3.1.0

# Install & build
npm install
npm run build

# Run (stdio — for Claude Desktop / Cursor)
node dist/index.js

# Or dev mode (no build needed)
npm run dev

Transports

Transport	Command	Port	Clients
stdio	node dist/index.js	—	Claude Desktop, Cursor, VS Code
SSE	node dist/sse-server.js	9002	Web clients, remote agents
Streamable HTTP	node dist/http-server.js	9003	Modern MCP clients (spec 2025-11-25)

---

Client Configuration

Claude Desktop

Edit ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows):

{
  "mcpServers": {
    "astra": {
      "command": "node",
      "args": ["/absolute/path/to/dist/index.js"],
      "env": { "ASTRA_LOG_LEVEL": "info" }
    }
  }
}

Cursor

Add to .cursor/mcp.json (project) or ~/.cursor/mcp.json (global):

{
  "mcpServers": {
    "astra": {
      "command": "node",
      "args": ["/absolute/path/to/dist/index.js"]
    }
  }
}

VS Code

Add to .vscode/settings.json:

{
  "mcp": {
    "servers": {
      "astra": {
        "type": "stdio",
        "command": "node",
        "args": ["${workspaceFolder}/dist/index.js"]
      }
    }
  }
}

Docker (remote SSE + HTTP)

docker compose up -d
# SSE: http://host:9002/sse
# HTTP: http://host:9003/mcp

---

MCP Tools (70)

Counts below are asserted by the CI stdio smoke test, not maintained by hand. Every tool declares a title and the four MCP tool annotations (readOnlyHint, destructiveHint, idempotentHint, openWorldHint), from a single table: src/tool-annotations.ts. The classification follows each handler's code, not its name — e.g. wm_encode is not read-only (it feeds the history wm_surprise reads), tcai_curiosity trains its predictor, np_count_spikes advances the simulated MEA clock. Only ovo_read, ovo_cycle and orch_cycle are open-world (OVOMIND live API when configured). tests/annotations.test.ts asserts that the table and tools/list match exactly. Hints are advisory, not a security boundary.

Core (12)

Tool	Title	Annotations
get_system_status	ASTRA System Status	📖 read-only
get_metrics	Real-time Metrics	📖 read-only
get_snn_state	SNN Engine State	📖 read-only
snn_step	Advance SNN Simulation	✏️ additive
snn_reset	Reset SNN Engine	⚠️ destructive · idempotent
inject_spikes	Spike Injection	✏️ additive
get_acm_score	ACM Proxy Engineering Index (not a measurement)	📖 read-only
check_ethics	IRB Neural Welfare Check	📖 read-only
set_parameter	Modify State Parameter	⚠️ destructive · idempotent · bounds-checked
get_platform_status	Bio-Computing Platforms	📖 read-only
export_snapshot	Full State Snapshot	📖 read-only
simulation_control	Simulation Control	✏️ non-destructive · idempotent

Domain families (58)

Family	Count	Scope	Guide
wm_*	6	JEPA World Model: encode, predict, plan (CEM), train, surprise	WORLD-MODEL.md
sensor_*	6	Untrained encoders inspired by V-JEPA 2 · A-JEPA · Koniku Kore (simulated) · cross-modal fusion	—
tcai_*	17	ACM cycle, workspace, emotion, memory, self-model, metrics, second-order loop	TCAI-INTEGRATION.md · SECOND-ORDER-LOOP-INTEGRATION.md
np_*	9	NeuroPlatform v2: status, stim config, triggers, spike queries, camera, closed loop	NEUROPLATFORM-INTEGRATION.md
ovo_*	6	OVOMIND affective exteroception bridge (sim by default; live adapter is a stub)	OVOMIND-INTEGRATION.md
orch_*	6	Orch OR substrate criterion, decoherence budget, classical surrogate gate	ORCH-OR-INTEGRATION.en.md · .fr.md
fcs_*	8	Substrate-constrained functionalism: 4-level framework, 17 species–function pairs in Pareto strata, per-substrate conformance audit, withdrawal conditions, negative-heuristic linter	FCS-INTEGRATION.en.md · .fr.md

MCP Resources (15)

URI	Description
astra://metrics/realtime	Live metrics from all subsystems
astra://snn/topology	Actual network architecture (reflects engine config)
astra://acm/state	Current consciousness proxy assessment vector
astra://ethics/welfare	IRB compliance and welfare report (mode-aware)
astra://snapshot/current	Complete state dump
astra://wm/latent	World Model latent embedding (current)
astra://wm/predictions	World Model rollout predictions
astra://sensors/state	Multimodal sensor pipeline state (visual · audio · olfactory · fusion)
astra://tcai/state	TCAI/ACM workspace, emotion, self-model & metrics
astra://tcai/second-order	Second-order self-evidencing loop telemetry (setpoint, model error)
astra://neuroplatform/state	NeuroPlatform bridge state (MEA activity, viability, coupling)
astra://fcs/framework	FCS four-level framework, core/belt partition and ASTRA coverage
astra://fcs/taxonomy	17 species–function pairs in their Pareto strata
astra://fcs/conformance	Per-substrate FCS conformance audit against live biomarkers
astra://fcs/references	Verified-DOI bibliography of the FCS series

MCP Prompts (10)

Pre-built workflow templates that orchestrate multi-tool sequences:

Prompt	Description
system-health-report	Orchestrates multiple tools into a comprehensive system report
snn-experiment	Controlled SNN experiment: reset → stimulate → observe STDP → assess proxies
ethics-stress-test	Progressive biomarker degradation: NORMAL → STRESS → DISTRESS → recovery
wm-experiment	World Model experiment: encode → predict → compare → plan
multimodal-experiment	Full multimodal sensor experiment: visual + audio + olfactory → fused → WM
tcai-consciousness-cycle	Guided ACM cycle: specialists → binding → ignition → broadcast → qualia → metrics
tcai-second-order-loop	Probe the second-order self-evidencing loop (setpoint regulation)
neuroplatform-experiment	Guided closed-loop protocol: read MEA → configure charge-balanced stim → trigger → observe
fcs-substrate-audit	Audit ASTRA's three substrates against the FCS taxonomy (no conformance score — prohibition 4)
fcs-belt-review	Review the protective belt against current strand outcomes and the declared revision order

---

Architecture

.github/workflows/
└── ci.yml                # GitHub Actions: build, test, Docker smoke-test

src/
├── index.ts              # stdio transport entry point
├── sse-server.ts         # SSE transport (Express) — exports createSseApp() for tests
├── http-server.ts        # Streamable HTTP transport (Express) — exports createHttpApp()
├── version.ts            # ASTRA_VERSION — single source of truth, consumed by all transports
├── lint-guard.ts         # Server-wide claim guard: lintClaim + lintFcs on every tool/resource payload
├── tool-annotations.ts   # MCP annotations for all 70 tools (single table, test-enforced)
├── bridge-state.ts       # Typed state contract shared by the wm/sensor/tcai/np tool families
├── server.ts             # MCP server factory (70 tools + 10 prompts + 15 resources)
│   ├── server-wm-tools.ts            # World Model JEPA (6 tools + 2 resources + 1 prompt)
│   ├── server-sensor-tools.ts        # Multimodal sensors (6 tools + 1 resource + 1 prompt)
│   ├── server-tcai-tools.ts          # TCAI/ACM (17 tools + 2 resources + 2 prompts, incl. closed-loop active inference)
│   ├── server-neuroplatform-tools.ts # NeuroPlatform v2 (9 tools + 1 resource + 1 prompt)
│   ├── server-ovomind-tools.ts       # OVOMIND affective bridge (6 tools)
│   ├── server-orch-tools.ts          # Orch OR criterion layer (6 tools)
│   └── server-fcs-tools.ts           # FCS layer (8 tools + 4 resources + 2 prompts)
├── engine/
│   ├── state.ts          # Reactive state store + parameter bounds registry
│   ├── snn.ts            # Layered SNN LIF+STDP engine (Map-indexed sparse weights, event-driven)
│   ├── acm.ts            # Consciousness proxy module (Φ̃ + GW̃ + PAD̃)
│   ├── ethics.ts         # IRB ethics monitor (mode-aware, biomarker thresholds)
│   ├── world-model.ts    # JEPA World Model engine (LeWM adapted)
│   ├── wm-simulation.ts  # WM simulation manager (replay buffer, auto-train)
│   ├── multimodal-sensors.ts # V-JEPA 2- / A-JEPA- / Koniku-inspired encoders (untrained) + fusion
│   ├── neuroplatform.ts  # FinalSpark NeuroPlatform v2 port + OrganoidMEA simulator
│   ├── ovomind.ts        # OVOMIND adapter (sim default; live adapter is a declared stub)
│   ├── simulation.ts     # Background tick loop
│   ├── fcs/              # FCS: taxonomy, levels, stratification (Pareto, dominance relation,
│   │                     #   sensitivity), conformance, negative-heuristic linter, withdrawal
│   │                     #   conditions, optogenetics (S-1.6 belt extension), references
│   └── tcai/             # ACM native port: global-workspace, oscillatory-binding, emotion,
│                         #   emotional-memory, self-model, second-order, active-inference,
│                         #   metrics, acm-bridge, orch-or, phenomenal-guard, types
└── utils/
    ├── logger.ts         # Structured logging (pino → stderr)
    └── rng.ts            # Global seeded PRNG (mulberry32, ASTRA_SEED)

tests/                    # 354 tests · 66 suites
├── astra.test.ts             # Unit: state, bounds, SNN, ACM, ethics, security
├── world-model.test.ts       # World Model: encoder, predictor, SIGReg, CEM, surprise
├── wm-simulation.test.ts     # WM simulation: buffer, training, planning, lifecycle
├── multimodal-sensors.test.ts # Sensors: V-JEPA, A-JEPA, Koniku, fusion, pipeline
├── tcai.test.ts              # TCAI/ACM: binding, GNW, memory, emotion, self-model, metrics
├── neuroplatform.test.ts     # NeuroPlatform: StimParam, OrganoidMEA, controllers, bridge
├── neuroplatform-e2.test.ts  # E2 'network-burst' spontaneous model (frozen parameters)
├── second-order.test.ts      # Second-order loop: setpoint regulation, production loop
├── aif-equivalence.test.ts   # TS↔NumPy active-inference golden equivalence
├── integration.test.ts       # Client SDK: tools, resources, prompts, workflow
├── transports.test.ts        # HTTP/SSE transport layer: session lifecycle, guards, regressions
├── fcs.test.ts               # FCS: strata, dominance relation, sensitivity, calcium binding, linters, S-1.6
├── lint-guard.test.ts        # Server-wide claim guard: blocking, exemption, every payload screened
├── annotations.test.ts       # MCP annotations: table ≡ tools/list, classification invariants
└── reproducibility.test.ts   # Seeded streams: same seed ⇒ same SNN and encoder outputs

configs/                  # Ready-to-use client configurations

Extracted to separate repositories: The v1 HTML dashboard (4 669 lines) and the legacy Node.js bridge config have been removed from this repo to keep it focused on the MCP server. See ASTRA-Unified-ResearchLab-MCP- for the original dashboard.

SNN Engine

Layered LIF+STDP — Configurable layered architecture. Default: 32 (input) → 64 (hidden_1) → 16 (hidden_2) → 16 (output) = 128 neurons.

Connectivity: feed-forward between adjacent layers (30%) + sparse recurrent within layers (10%). Weights stored as sparse adjacency lists, not dense matrices.

Biophysical parameters: τ_m = 20ms, V_th = −50mV, V_reset = −70mV, refractory = 2ms. Background noise range [10, 22] mV produces ~2 spikes/step at steady state with all neurons active. STDP: A+ = 0.01, A− = 0.012, τ± = 20ms, event-driven (processes only spiking neurons per timestep).

The SNN topology resource (astra://snn/topology) dynamically reports the actual engine configuration, including layer sizes, synapse count, connectivity parameters, and weight storage type (Map-indexed sparse adjacency lists).

ACM — Consciousness Proxy Module

⚠ Methodological disclaimer: The metrics below are computational proxies inspired by the referenced theories. They are not faithful implementations. See source code comments for full details.

Composite engineering index: ACM = α·Φ̃ + β·GW̃ + γ·PAD̃ (default: α=0.40, β=0.35, γ=0.25). Conventional weights over three heterogeneous proxies lacking a common scale: no class, level or label is derived from it (FCS prohibitions 1 and 4; the ABSENT…FULL scale of ≤ v3.1.0 is withdrawn), and every payload carries this status in aggregationStatus.

Component	Basis	Inspired by	What it actually measures
integrationProxy (Φ̃)	Active fraction + mean firing rate + synaptic heterogeneity	IIT (Tononi)	Network participation and complexity proxy. True Φ is NP-hard to compute.
broadcastProxy (GW̃)	Cross-layer firing rate synchrony (CV-based)	GWT (Baars)	Uniform activation across layers. Does not model competitive coalitions or ignition.
arousalProxy (PAD̃)	Spike rate + bio coupling + energy	PAD (Mehrabian)	Arousal dimension only. Pleasure and Dominance are not computed.

Ethics IRB Monitor

IRB compliance level N3 (100K–1M neurons). Four biomarkers with three-state classification.

Mode-aware: In sim mode, reports include explicit disclaimers that data is synthetic and irbRequired is false. In live mode, DISTRESS triggers mandatory IRB notification.

Biomarker	Normal	Stress	Critical
Cell viability	≥ 90%	80–90%	< 80%
Firing rate (median per unit)	0.14–0.63 Hz	0.07–0.14 or 0.63–1.3 Hz	< 0.07 or > 1.3 Hz
ATP/ADP	≥ 3.0	2.0–3.0	< 2.0
Intracellular free Ca²⁺	< 100 nM	100–200 nM	≥ 200 nM

The firing-rate interval is the observed range of the eight DANDI 001603 organoids confronted in empirical/ (E1, E2), with the factor-2 band of the preregistrations; it is a descriptive reference interval from one dataset, not a validated welfare criterion (v3.1.1; the former 15–45 Hz range classed every one of those organoids as in distress). Intracellular Ca²⁺ is a second messenger: it is bound to no FCS pair.

Parameter Bounds

The set_parameter tool validates all numeric inputs against a bounds registry to prevent injection of absurd values (negative percentages, Infinity, NaN). Bounds are defined per parameter path — see src/engine/state.ts for the complete registry.

---

Testing

# Full suite
npm test

# Unit tests only
node --import tsx --test tests/astra.test.ts

# Integration tests only (Client SDK)
node --import tsx --test tests/integration.test.ts

# Targeted suites
npm run test:tcai          # TCAI/ACM
npm run test:np            # NeuroPlatform v2
npm run test:so            # second-order loop
npm run test:wm            # World Model
npm run test:sensors       # multimodal sensors
npm run test:transports    # HTTP + SSE transport layer
npm run test:fcs           # FCS layer
npm run test:annotations   # MCP tool annotations
npm run test:repro         # seeded reproducibility
npm run test:guard         # server-wide claim guard

# Static gates
npm run build              # tsc strict (Node16 ESM)
npm run lint               # ESLint 9 flat config
npm run golden:check       # TS↔NumPy active-inference golden (requires python3 + numpy)

# MCP Inspector
npm run inspect

Full suite: 354/354 passing (230 engine/integration + 8 E2 model + 12 transport-layer + 86 FCS + 7 annotations + 6 reproducibility + 5 claim guard), 0 TypeScript errors (strict, Node16 ESM), 0 ESLint errors. Verified on Node 20 and Node 22 in CI.

Development

npm run dev        # stdio (no build)
npm run dev:sse    # SSE on :9002
npm run dev:http   # HTTP on :9003
npm run watch      # TypeScript watch mode

Environment Variables

Variable	Default	Description
ASTRA_LOG_LEVEL	info	debug, info, warn, error, silent
ASTRA_SSE_PORT	9002	SSE transport port
ASTRA_SSE_HOST	127.0.0.1	SSE bind address
ASTRA_HTTP_PORT	9003	Streamable HTTP port
ASTRA_HTTP_HOST	127.0.0.1	Streamable HTTP bind address
ASTRA_CORS_ORIGIN	*	CORS allowed origin
ASTRA_SEED	20260923	Seed of the global PRNG (unsigned 32-bit). Same seed ⇒ same random streams; wall-clock-driven ticks still interleave differently — for bit-level replay keep the simulation loop stopped and drive it with snn_step.

Bind address defaults to loopback. Both HTTP transports bind 127.0.0.1 so a local server is not exposed to the network by default (the permissive CORS default would otherwise widen the attack surface). The Dockerfile and docker-compose.yml set ASTRA_*_HOST=0.0.0.0 explicitly, since a container must accept traffic from outside its own namespace. Set it yourself for any non-container remote deployment — and set ASTRA_CORS_ORIGIN to a concrete origin when you do.

---

Scaling Notes

The default 128-neuron configuration is designed for interactive demonstration. To scale toward the aspirational 256→512→256→128 (1 152 neurons) architecture:

1. Pass custom layers to SNNEngine: new SNNEngine({ layers: [{ name: 'input', size: 256 }, ...] })
2. Event-driven STDP scales as O(spikes × average fan-out), not O(N²)
3. Map-indexed adjacency lists provide O(1) weight lookup per synapse
4. Sparse storage keeps memory proportional to actual synapses (~18 KB at 128 neurons vs 64 KB dense)
5. Consider increasing intervalMs in the simulation loop for larger networks
6. For >10K neurons, a Rust/WASM or Lava SDK backend is recommended

---

License

MIT — © 2026 Christophe Jean Legros, Geneva — applies to everything in this repository except the directory below.

Third-party code under a different licence. python/the_consciousness_ai/ is vendored from tlcdv/the_consciousness_ai and remains under its own Non-Commercial Open Source License (see python/the_consciousness_ai/LICENSE.md): non-commercial use only, attribution to tlcdv required, no sublicensing. The MIT licence above does not extend to it. Nine files of src/engine/tcai/ port parts of that project to TypeScript; pending a legal assessment they are treated conservatively as subject to its non-commercial terms. Details, file list and status: THIRD_PARTY_NOTICES.md.

Citing and reviewing. Releases are archived on Zenodo. Cite the version you used: v3.1.1 is doi:10.5281/zenodo.23196960; the concept DOI doi:10.5281/zenodo.23196959 covers all versions and resolves to the latest. Metadata: CITATION.cff. External review is invited through REVIEW.md; substrate-level predictions are drafted for preregistration in PREREGISTRATION.md.

Assistance Multi IA · Assistant-Multi-IA@proton.me

References

• Model Context Protocol · Spec 2025-11-25
• MCP TypeScript SDK
• FinalSpark · Cortical Labs · Koniku
• Intel Lava / Loihi 2
• Gerstner & Kistler (2002) "Spiking Neuron Models"
• Tononi (2004) "An information integration theory of consciousness" — BMC Neuroscience
• Baars (1988) "A Cognitive Theory of Consciousness" — Cambridge University Press
• Mehrabian (1996) "Pleasure-Arousal-Dominance: A General Framework" — Current Psychology