v5.6.0 · Open source · TUI v9 · 21 MCP tools
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c4reqber

The cognitive exoskeleton for humans and AI agents.
Think. Simulate. Prove. Discover.

SHIFT PARADIGMS

Z₃³ COGNITIVE EXOSKELETON · 27 STATES · 6 OPERATORS · 47 SOURCES · 38 ENGINE BRIDGES · 21 MCP TOOLS · O₀→O₁→O₂ OBSERVER · 23 MPs

AGPL-3.0 · BYOK · Multi-Prompt Router · Terminal-First · OpenRouter · XAI · Mistral · Moonshot · DeepSeek · Liquid · NVIDIA · YandexGPT · Ollama · LM Studio · MLX

27
Cognitive States
6
C4 Operators
47
Knowledge Sources
38
Simulation Engines
21
MCP Tools
9924
Tests Collected

What is c4reqber?

In plain language — no jargon required.

1

What

A terminal-first research assistant. You ask a scientific question — c4reqber searches 51 literature sources, runs simulations, checks proofs, and writes a gated research proposal. Not a chatbot. A pipeline.

2

Install

One command. Python 3.11+. Bring your own API key (OpenRouter, Mistral, etc.). Optional GPU for heavy sims.

3

Use

blast solve "your question" for a one-shot run. blast turbo for paradigm proposals. blast tui for the visual cockpit. blast serve --mcp for AI agents.

Full guide →

Agents Can Talk. But Can They Think?

AI agents have language. They lack cognition. c4reqber is the scientific body for the agentic mind.

No Simulation

LLMs generate hypotheses but cannot test them. No physics engine, no statistical validation, no ground truth.

No Verification

ChatGPT "proves" theorems by generating convincing text. Formal verification requires Lean4, Coq, Dafny.

No Blind-Spot Detection

Agents cannot recognize their own observational biases or identify gaps in their reasoning. c4reqber uses O₀→O₁ observer shifts to surface blind spots automatically.

No Scientific Rigor

Falsifiability, real citations, reproducibility — the foundation of science. Absent from most agent frameworks.

c4reqber solves all four. Formal verification + 38 simulation engine bridges + Z₃³ cognitive topology + real citations + O₀→O₁→O₂ meta-cognitive observer.

The Only AI Cognitive Exoskeleton

Not features. Cognitive organs. Each module is a real implementation.

Z₃³ Cognitive Topology

27 discrete cognitive states across Time, Scale, and Agency dimensions. Every query is mapped, tracked, and navigable.

Z₃³Theorem 9Theorem 11

Formal Verification Engine

Lean4, Coq, Dafny, Agda, Z3, Hoare logic — your hypotheses don't just claim, they prove.

Lean4CoqDafnyZ3

38 Simulation Engines

Molecular dynamics (GROMACS, OpenMM), quantum (PySCF), CFD (OpenFOAM), neuro (NEURON), and more.

GROMACSOpenFOAMPySCFNEURON

47 Knowledge Sources

arXiv, PubMed, Semantic Scholar, OpenAlex, Europe PMC, Crossref, Zenodo, ClinicalTrials.gov, GBIF, NASA Earthdata, Materials Project, Kaggle, OpenFDA, ORCID, and other configured sources. MultiSourceSearcher with circuit breaker and semantic dedup.

arXivPubMedDOICircuit Breaker

Automated Dissertation Generator

LaTeX + BibTeX + Markdown + JSON + HTML exports. Citation verifier with hallucination detection. Zenodo DOI upload; arXiv/bioRxiv = LaTeX package generation only (no auto-submit API).

LaTeXBibTeXAnti-Hallucination

MCP Server — 21 Tools

Expose full C4REQBER capability to AI agents. JSON Schema compliant. stdio JSON-RPC.

21 ToolsJSON SchemaClaude

Observer Position Shifts

O₀→O₁ self-diagnostic after synthesis detects blind spots. O₁→O₂ meta-reflection on stagnation derives alternative C4 routes. Keyword-driven axis shifts + deterministic fallback.

O₀→O₁→O₂Blind SpotsStagnation

23 Core Metaprograms

Multi-perspective analysis via 23 perceptual filters across 9 dimensions (thinking, feeling, doing, relating, perceiving, time, chunking, direction, reason). Pipeline step s4 rotates problems through 3 keyword-matched profiles.

23 MPs9 DimensionsMP Rotation

Research Audiences

From hard science to social sciences — c4reqber adapts to your domain.

Hard Science

Physics, chemistry, biology, materials. TRIZ + 38 simulation engine bridges + formal verification.

GROMACSOpenFOAMPySCFLean4

Psychology & Social Sciences

CBT meta-analysis, organizational behavior, political psychology. Causal inference + agent models.

RCTSEMAgent-based

Clinical Research

RCT design, biomarkers, drug-drug interactions. PubMed + ClinicalTrials.gov + STRING.

PubMedSTRINGTrials
🌎

Climate & Ecology

Biodiversity, climate modeling, ocean dynamics. GBIF + NASA Earthdata + WRF.

GBIFNASAWRF

Law & Policy

Legal reasoning, precedent analysis, regulatory impact. Multi-jurisdiction + temporal reasoning.

PrecedentRegulatoryTemporal

C4-META vs. The Field

Discrete group-theoretic cognitive space. Not neural networks. Not symbolic rules. Mathematical topology.

ModelC4-METASOARACT-RGWTIITPMCSFConSpacesFreudPlato
Dimensions3 (Z₃)221N17333
States27 (discrete)SymbolicChunksBroadcastΦContinuousRegionsPsychoanal.Forms
RepresentationDiscrete (Z₃³)Symbolic (rules)Symbolic (chunks)Continuous (broadcast)Continuous (Φ)Continuous (17D vectors)Geometric (regions)PsychoanalyticDialectical (forms)
FormalismGroup theoryProductionProductionDescriptiveInfo. theoryVectorsGeometryClinicalPhilosophy
VerificationLean4 + CoqNoNoNoNoNoNoNoNo
NavigationTheorem 9RulesRulesNoNoGradientPathsNoNo
ReachabilityTheorem 11NoNoNoNoNoNoNoNo
Cross-DomainUniversalAI onlyCognitiveConscious.Conscious.NLP onlySpatialNoNo
Open SourceAGPL-3.0BSDBSDNoNoNoMITNoNo
Peer-ReviewedarXiv (soon)YesYesYesYesYesYesNoNo

c4reqber vs. The Market

Not an LLM wrapper. A cognitive operating system.

Productc4reqberElicitConsensusScite.aiPerplexityChatGPT DRGemini DRSemantic ScholarGNoMEA-LabAlphaFold3InsilicoRecursionSchrödingerCradleAI ScientistOpenAlexLean4+AIDafny+AINeo4j+KGCOMSOL+AI
Lit. Review
Hypothesis
Simulation
Formal Verify
Multi-Domain
Auto Publish
WASM Runtime
MCP Server
Open SourceAGPL-3.0
PriceFree (BYOK)$29-49/m$7-49/m$20-79/m$20/m$20-200/mPlanFreeFreeResearchFree/CommEnterpriseEnterpriseEnterpriseEnterpriseFreeFreeFreeFreeEnterpriseEnterprise

● Yes · ○ No · ◐ Partial

2026 AI-for-science entrants — what they actually are

These launches are not equivalent. Claude Science is the closest workflow-level competitor; GPT‑Rosalind competes in the life-sciences vertical; Prism primarily competes with the writing and publication layer.

ProductActual scopeWhere it leadsLimits versus c4reqber
Claude SciencePaid beta scientific workbench with a general coordinator, 60+ skills/connectors, and local, SSH, or HPC execution. Broad in principle; currently strongest in computational life sciences.Reproducible artifacts with full provenance, native scientific figures, compute orchestration, and a reviewer agent.Closed and paid; current domain pack is biology-heavy. No announced formal-proof stack, C4/TRIZ reasoning, or broad built-in simulation catalogue.
GPT‑RosalindControlled-access model for biology, drug discovery, and translational medicine, with 50+ scientific tools available through a Codex plugin.Purpose-trained biochemical reasoning across proteins, genes, chemistry, experimental planning, and tool-heavy workflows.Qualified-access life-sciences preview, not a general cross-domain workbench; no announced formal-verification stack.
PrismFree cloud LaTeX workspace for scientific writing and collaboration with GPT‑5.2 in the document context.Manuscript-wide editing, equations, citations, figures, and real-time collaboration without local LaTeX setup.Not an autonomous researcher; no lab/HPC orchestration, domain simulation, causal pipeline, or formal verification.

Assessment dated July 13, 2026. Primary sources: Claude Science · GPT‑Rosalind · Prism.

Pipeline Phases — Model per Stage

7 phases. Each gets its own LLM model, plugins, and cognitive strategy.

PhaseStageModelPlugins
AC4 Cognitive Framingclaude-sonnet-4.6info_theory, dim_reduction
BKnowledge Searchqwen-2.5-72btext_distance, graph_metrics
CGap Analysisqwen-2.5-72btimeseries, text_distance
DHypothesis Generationclaude-sonnet-4.6SWOT, Delphi, Red Team
ESimulation & Verification(compute plugins)Monte Carlo, DFT, PCA, Nelder-Mead
FDissertationclaude-sonnet-4.6hash_fingerprint
GQuality Controlgpt-4o-ministat_tests, dist_analyzer

Models are fully configurable per phase — swap them in your config.

From Question to Discovery

7 stages. Each transforms, validates, and enriches. No black boxes.

🔒

Sanitize

Strip HTML, normalize unicode, block injection

C4 Space

Fingerprint into Z₃³ cognitive coordinate

📖

Knowledge

47 sources + QZRF/CDI analysis

💡

Hypothesis

Multi-agent debate + TRIZ templates

Sim + Verify

38 engines + Lean4/Coq/Dafny

Quality Gates

8-gate scoring + self-critique

📝

Output

Dissertation, article, code, report

Paradigm Shifts Detected

Real results. Real citations. Real verification.

ALREADY_SHIFTED 100% confidence

Sleep as Active Maintenance

Detected that the hypothesis "sleep is active maintenance" has already been shifted by existing research. Consensus meter: 93.3%.

Lean4: proof_skeleton.generated
Sources: 10 verified citations
Verdict: ALREADY_SHIFTED
SHIFTED 66.67% confidence

Language Horizontal Gene Transfer

Full article (4,985 chars). 10 sources. Bayesian AUC: 0.32. Uncertainty: 0.34. Passed ALL gates.

Article: LANG_EVOLUTION_DISSERTATION.md
Sources: 10 · Bayesian AUC: 0.32
Verdict: SHIFTED
NOT_SHIFTED 10,000× speedup

Consciousness Modeling: C4-IIT Bridge

Full dissertation (11,200 chars). 15 sources. Closed-form Φ approximation via C4 graph metrics. 10,000× speedup vs exact IIT 3.0. Pearson r = 0.94.

Dissertation: dissertation_09_consciousness.md
Sources: 15 · Pearson r: 0.94 · Speedup: 10,000×
Verdict: NOT_SHIFTED

Multi-Agent Debate

Analyst, Scientist, Critic, Synthesizer. Each with a distinct cognitive role.

🔬

Analyst

Breaks problem into entities, maps dependencies, ranks by centrality. SystemAnalyzer extracts the structure.

💡

Scientist

Generates hypotheses via TRIZ, C4 navigation, literature gaps. Explores the unknown systematically.

📝

Critic

Nature reviewer persona. Falsification engine. Platt's Strong Inference. Finds the holes before publication.

Synthesizer

Resolves contradictions (CDI), builds consensus, writes dissertation. Consensus meter: 93.3% typical.

MCP Native — 21 Tools

JSON Schema compliant. stdio JSON-RPC. Any MCP host — Claude, Cursor, Cline, Continue.dev, and beyond.

c4_solve

12-stage discovery pipeline

c4_search

47 knowledge sources

c4_triz

Contradiction resolution

c4_fingerprint

Z₃³ state classification

c4_verify

Lean4/Coq/Dafny check

c4_prove

LLM-based proof gen

c4_transfer

Cross-domain isomorphism

c4_simulate

38 engine adapters

c4_bayesian

MCMC / BMA inference

c4_causal

Do-calculus discovery

c4_export

MD/JSON/BibTeX/LaTeX

c4_social

Multi-platform publish

c4_chain

C4 discovery chain

c4_meta

Meta-cognitive reflection

blast_solve

UniversalSolvePipeline

blast_turbo

Paradigm dissertations

blast_flash

Quick LLM + USP analysis

blast_turbofactory

Parallel pipeline factory

c4_autoresearch

Karpathy-style ML loop

blast_auto

Auto-router dispatch

# Start MCP server blast serve --mcp # Tool schema (auto-synced) {"name": "c4_solve", "inputSchema": {...}, "outputSchema": {...}}

TUI v9 Experience

38 sim engine bridges, 9 verifiers, capabilities overlay, command palette. The simulation/verification cockpit is in the terminal — not a fallback, the primary interface.

c4reqber — TUI v9 (capabilities overlay)
⏚ Simulation Capabilities (Darwin arm64)
● newton Apple M3 Pro · 18 GB unified (49 patterns)
● jaxsim MPS (12 patterns)
● torchsim MPS (9 patterns)
● openmm CPU/Metal — biology, protein_folding
● vinda CPU
● mesa CPU
○ fenicsx (no arm64 wheel)
ⓘ conda install -c conda-forge fenics-dolfinx
✓ 38 engine bridges · 9 verifiers across 6 domains
_
: Command palette Ctrl+Shift+C: Capabilities Ctrl+Shift+D: Debug Ctrl+B: Status bar j/k: Focus card Enter: Expand i: Install hint f: Fallback chain Ctrl+Shift+K: Setup Hub Ctrl+Shift+S: Social publish Shift+A: Research agenda Ctrl+Shift+M: Models & council

Social Publishing — Multi-Channel

Discovery → draft → blast social publish. Zenodo DOI + every configured social channel (skipped if no API key).

📰
arXiv
📝
bioRxiv
💾
Zenodo
💬
Reddit
📢
Discord
💬
Slack
Telegram
🐦
Twitter/X
🌌
Bluesky

Workflow: Discovery → draft → Zenodo → ORCID (optional) → social post to configured platforms. arXiv: LaTeX package generation only.

Zenodo = real DOI upload. arXiv = LaTeX package only. bioRxiv = not yet wired. Each social channel skipped without API key.

TUI: Ctrl+Shift+S — drafts, health check, publish

CLI: blast social publish · blast social post --id … --platform mastodon

Full guide: docs/SOCIAL_PUBLISHING.md on GitLab

3 Commands to Discovery

Three commands. Five minutes. Your first discovery.

# 1. Install pip install c4reqber # 2. Set your key export OPENROUTER_API_KEY=sk-or-... # 3. Run (CLI or TUI v9 Cockpit) blast solve "quantum biology in photosynthesis" blast tui # feed-driven discovery UI blast tui --demo --story=crispr # no backend required # → paradigm-shifting hypothesis + dissertation + citations # Model-per-stage config blast config --tier budget --save # $0.002/pipeline blast config --tier premium --save # Claude Opus everywhere blast config --set D=gemma4:26b # Local model for hypotheses blast config keys --assign OPENROUTER_API_KEY=sk-or-... # secrets.env

Academic tip: Run with --verify flag to auto-invoke Lean4/Coq for theorem-checking.

36 Scientific Computing Engines

5 internal GPU engines + 31 open-source bridges. From molecular dynamics to climate modeling.

DomainEngineDescriptionStatus
PhysicsNewtonClassical mechanics, N-body, orbitalBuilt-in GPU
PhysicsJaxSimDifferentiable physics, roboticsBuilt-in GPU
PhysicsTorchSimPyTorch-native material simulationBuilt-in GPU
PhysicsNVIDIANative CUDA kernels (cuBLAS, cuDNN)Built-in GPU
PhysicsSchrQuantum electrodynamics solverP1 Bridge
PhysicsFEniCSxFinite element method PDE solverP1 Bridge
PhysicsOpenFOAMCFD, turbulence, multiphaseP1 Bridge
ChemistryPySCFQuantum chemistry, DFTP1 Bridge
ChemistryPsi4Ab initio quantum chemistryP1 Bridge
ChemistryQuantum ESPRESSOPlane-wave DFTP1 Bridge
ChemistryLAMMPSLarge-scale atomic/molecular MDP1 Bridge
ChemistryGROMACSMolecular dynamicsP1 Bridge
ChemistryVinaProtein-ligand dockingP1 Bridge
BioOpenMMGPU molecular dynamics, protein foldingBuilt-in GPU
BioNEURONBiophysical neuron simulationP1 Bridge
BioBrian2Spiking neural networksP1 Bridge
BioJaxleyDifferentiable biophysical neuronsP1 Bridge
BioTelluriumSystems biology simulationP1 Bridge
BioCOPASIBiochemical network simulationP1 Bridge
BioMDAnalysisMD trajectory analysisP1 Bridge
BioBoolNetGene regulatory networksP1 Bridge
BioCobraMetabolic flux analysisP1 Bridge
BioSLiMPopulation genetics simulationP1 Bridge
ClimateWRFWeather research & forecastingP1 Bridge
ClimateXarrayClimate data analysisP1 Bridge
AstronomyAMUSEAstrophysics multiphysics frameworkP1 Bridge
AstronomyReboundPlanetary dynamics N-bodyP1 Bridge
RoboticsMuJoCoContact dynamics simulatorP1 Bridge
RoboticsPyBulletRobotics simulation engineP1 Bridge
Math & StatsDiffEqPyODE/PDE solver suiteP1 Bridge
Math & StatsModelingToolkitSymbolic modeling and simulationP1 Bridge
Math & StatsJAX-LABLattice Boltzmann methodP1 Bridge
Math & StatsTaichiGPU simulation frameworkP1 Bridge
Math & StatsMesaAgent-based modeling frameworkP1 Bridge
Math & StatsSimPyDiscrete event simulationP1 Bridge
Math & StatsJAX-MDDifferentiable molecular dynamicsP1 Bridge

5 Built-in GPU engines · 31 Python-native open-source bridges · Full list in src/simulations/

47 Knowledge Sources — Real Citations

No hallucinated references. Every citation is verified against live databases with DOI.

Search Engines

🔍

Brave Search

Web + academic · 6B+ pages

API key
🔍

Exa.ai

Neural search · Semantic

API key
🔍

Tavily

AI search · Academic focus

API key
🔍

Semantic Scholar

Academic · 200M+ papers

Free
🔍

CORE

Open access · 10M+ full-text

API key
🔍

BASE

Academic · 150M+ docs

API key
🔍

OA.mg

Open access · 250M+ papers

API key
🔍

Unpaywall

OA articles · 40M+ records

API key
🔍

Lens.org

Scholarly + patents · 225M+

API key

Research Databases

General Science
arXivPubMedEurope PMCOpenAlexCrossrefDataCiteZenodoDOAJDBLPFigshareOpenReviewre3data
Biology & Medicine
NCBI E-utilsPubChemChEMBLSTRINGClinicalTrials.govAllen BrainOpenFDA
Climate & Earth
GBIFUSGSNASA Earthdata
Physics & Math
INSPIRE-HEPCERN Open DataMaterials ProjectAFLOWOEIS
Patents
USPTO PatentsViewLens.org
Data & ML
UCI MLKaggleHarvard DataverseHuggingFace Datasets
Knowledge Graphs
ConceptNetWikidata
Regional
CyberLeninkaMath-Net.RuRSCICiNii
Social & Code
SciMaticarXiv.ggGitHubDatasets

9 Formal Verification Backends

Your hypotheses don't just claim — they prove. Auto-selected by domain.

λ

Lean4

Dependent type theory for mathematics

π

Coq

Inductive proofs for hardware verification

Dafny

Imperative programs with pre/post-conditions

Agda

Intuitionistic type theory

Z3

SMT solver for constraint satisfaction

{}

Hoare

Logic for imperative program correctness

CVC5

Industrial SMT solver (SMT-LIB2)

TLA+

Temporal logic for concurrent systems

Alloy

Relational models with bounded analysis

OS & System Requirements

macOS and Linux are tested and supported. Windows is not tested. External engines require separate installation.

OS Compatibility Matrix

macOS✓ Tested
Linux✓ Tested
Windows✗ Not tested · WSL2 may work

Minimum Requirements

RAM4 GB (8 GB rec)
CPU2 cores (4+ for sim)
Disk2 GB + engines separately
GPUOptional · Apple Silicon / CUDA

PyPI · c4reqber · pip install -U c4reqber

Note: pip install c4reqber installs the Python package + CLI only. External simulation engines (GROMACS, OpenFOAM, etc.) require separate installation per engine. See GPU Setup.

5 Cost Tiers

From $0.002 to $0.11 per full pipeline run. Configure per phase.

Budget
$0.002/run
DeepSeek V4-Flash
Premium
$0.11/run
Claude Opus + Gemini
Local
$0/run
Qwen 3.6 + Gemma 4

What Is Next

Continuous delivery of simulation engines, AI integrations, and verification backends.

v5.5 — Now
✓ Mypy baseline tracked (56 errors, regression-gated) ✓ MCP 21 tools with JSON Schema ✓ Virtual Bio + GPU auto-detect ✓ 38 simulation engine bridges integrated ✓ 9908+ tests passing
v5.6 — Q3 2026
✓ TUI v9 simulation surface: capabilities overlay (38 engine bridges + 9 verifiers) ✓ CardSimulation kind with engine/verdict/fallback chain/install hint ✓ Command palette (:) with 35+ fuzzy-matched commands ✓ Typed SSE decoder for sim_started/sim_finished/sim_skipped events ✓ 4 new sim achievements (Sim Explorer, Devil's Advocate, Fallback Chef, Cloud Native) ✓ Adaptive layout (T0/T1/T2/T3 tiers) + status bar + debug overlay ✓ Per-card expansion (Enter to see FullBody, Esc to collapse) ✓ Feed.jsonl persistence + resume on launch ✓ 132 golden snapshots (6 fixtures × 22 scenarios) ✓ 100% i18n parity across 7 languages via regen_i18n.py ✓ Solarized-dark color profile (warm low-blue, easy on eyes) ✓ 7th color profile: 7 total (default, hc, prot, deut, trit, mono, solarized) ✓ Theme helper: real colorMap integration across header/status bar/cards ✓ Per-card sim actions: i (install hint), f (fallback chain), o (open plot) ✓ Verdict chips on hypothesis cards (✓/✗/? color-coded) ✓ Effects perf: Rain grid pooled (was 720k allocs/sec → 0) ✓ Effects bug: Burst per-particle fade (was using b.parts[0] for all cells) ✓ Wizard bug: F-13 fix — wizard now actually advances through 3 steps ✓ F-15 cost: header reads from sim cost events, not fake tick ticker ✓ Dead code cleanup (6 modules + orphaned tests removed) ✓ 14 API keys wired into MultiSourceSearcher ✓ Pydantic V2 migration (ConfigDict, field_validator) ✓ Citation verifier with hallucination detection ✓ TUI v8 Cube Mascot rewrite + Go audit (staticcheck 0) ✓ Observer Position Shifts O₀→O₁→O₂ integrated ✓ 23 Core Metaprograms in pipeline step s4 ✓ Cost tracker reset per solve() call
v5.7+ — 2027
○ JuliaDiff auto-differentiation ○ LangGraph state-machine agents ○ Unsloth local LLM fine-tuning ○ vLLM high-throughput inference ○ ChromaDB / LanceDB RAG layer ○ CrewAI multi-agent orchestration

Ready to Shift Paradigms?

One command. One dissertation. One paradigm shift.

AGPL-3.0 · BYOK · No data retention · Self-hostable