c4reqber
The cognitive exoskeleton for humans and AI agents.
Think. Simulate. Prove. Discover.
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 Meta-Reflection
Agents lack meta-cognition. They cannot track their own thinking state or reconfigure strategy.
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.
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.
Formal Verification Engine
Lean4, Coq, Dafny, Agda, Z3, Hoare logic — your hypotheses don't just claim, they prove.
38 Simulation Engine Bridges
Molecular dynamics (GROMACS, OpenMM), quantum (PySCF), CFD (OpenFOAM), neuro (NEURON), and more.
47 Knowledge Sources
arXiv, PubMed, Semantic Scholar, OpenAlex, Europe PMC, Crossref, Zenodo, ClinicalTrials.gov, GBIF, NASA Earthdata, and other configured sources.
Automated Dissertation Generator
LaTeX + BibTeX + Markdown + JSON + HTML exports. Ready for arXiv, bioRxiv, or your advisor's desk.
MCP Server — 21 Tools
Expose full C4REQBER capability to AI agents. JSON Schema compliant. stdio JSON-RPC.
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.
Psychology & Social Sciences
CBT meta-analysis, organizational behavior, political psychology. Causal inference + agent models.
Clinical Research
RCT design, biomarkers, drug-drug interactions. PubMed + ClinicalTrials.gov + STRING.
Climate & Ecology
Biodiversity, climate modeling, ocean dynamics. GBIF + NASA Earthdata + WRF.
Law & Policy
Legal reasoning, precedent analysis, regulatory impact. Multi-jurisdiction + temporal reasoning.
C4-META vs. The Field
Discrete group-theoretic cognitive space. Not neural networks. Not symbolic rules. Mathematical topology.
| Model | Formalism | C4-META | SOAR | ACT-R | GWT | IIT | PMCSF | ConSpaces | Freud | Plato |
|---|---|---|---|---|---|---|---|---|---|---|
| Dimensions | Dimensions | 3 (Z₃) | 2 | 2 | 1 | N | 17 | 3 | 3 | 3 |
| States | States | 27 (discrete) | Symbolic | Chunks | Broadcast | Φ | Continuous | Regions | Psychoanal. | Forms |
| Representation | Representation | Discrete (Z₃³) | Symbolic (rules) | Symbolic (chunks) | Continuous (broadcast) | Continuous (Φ) | Continuous (17D vectors) | Geometric (regions) | Psychoanalytic | Dialectical (forms) |
| Formalism | Formalism | Group theory | Production | Production | Descriptive | Info. theory | Vectors | Geometry | Clinical | Philosophy |
| Verification | Verification | Lean4 + Coq | No | No | No | No | No | No | No | No |
| Navigation | Navigation | Theorem 9 | Rules | Rules | No | No | Gradient | Paths | No | No |
| Reachability | Reachability | Theorem 11 | No | No | No | No | No | No | No | No |
| Cross-Domain | Cross-Domain | Universal | AI only | Cognitive | Conscious. | Conscious. | NLP only | Spatial | No | No |
| Open Source | Open Source | AGPL-3.0 | BSD | BSD | No | No | No | MIT | No | No |
| Peer-Reviewed | Peer-Reviewed | arXiv (soon) | Yes | Yes | Yes | Yes | Yes | Yes | No | No |
c4reqber vs. The Market
Not an LLM wrapper. A cognitive operating system.
| Product | Cognition | ChatGPT | Claude | Perplexity | Elicit | Consensus | scite | Semantic | ResearchRabbit | ConnectedPapers | Galactica | Minerva | AlphaProof | AlphaGeometry | FunSearch | c4reqber |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Lit. Review | Lit. Review | ● | ● | ● | ● | ● | ● | ● | ● | ● | ● | ○ | ○ | ○ | ● | |
| Hypothesis | Hypothesis | ● | ● | ○ | ● | ○ | ○ | ○ | ○ | ○ | ● | ○ | ○ | ● | ● | |
| Simulation | Simulation | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ● | |
| Formal Verify | Formal Verify | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ● | ● | ○ | ● | |
| Multi-Domain | Multi-Domain | ● | ● | ● | ○ | ○ | ○ | ○ | ○ | ○ | ● | ○ | ○ | ○ | ● | |
| Auto Publish | Auto Publish | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ● | |
| WASM Runtime | WASM Runtime | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ● | |
| MCP Server | MCP Server | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ● | |
| Open Source | Open Source | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | AGPL-3.0 | |
| Price | Price | $20/m | $20/m | $20/m | $0 | $0 | $0 | $0 | $0 | $0 | Dead | Internal | Internal | Internal | ~$0.35/run |
● Yes · ○ No · ◐ Partial
Pipeline Phases — Model per Stage
7 phases. Each gets its own LLM model, plugins, and cognitive strategy.
| Phase | Stage | Model | Plugins |
|---|---|---|---|
| A | C4 Cognitive Framing | claude-sonnet-4.6 | info_theory, dim_reduction |
| B | Knowledge Search | qwen-2.5-72b | text_distance, graph_metrics |
| C | Gap Analysis | qwen-2.5-72b | timeseries, text_distance |
| D | Hypothesis Generation | claude-sonnet-4.6 | SWOT, Delphi, Red Team |
| E | Simulation & Verification | (compute plugins) | Monte Carlo, DFT, PCA, Nelder-Mead |
| F | Dissertation | claude-sonnet-4.6 | hash_fingerprint |
| G | Quality Control | gpt-4o-mini | stat_tests, dist_analyzer |
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 engine bridges + Lean4/Coq/Dafny
Quality Gates
8-gate scoring + self-critique
Output
Dissertation, article, code, report
Output Examples Gallery
6 export formats. Auto-detected by keywords.
Paradigm Shifts Detected
Real results. Real citations. Real verification.
Sleep as Active Maintenance
Detected that the hypothesis "sleep is active maintenance" has already been shifted by existing research. Consensus meter: 93.3%.
Sources: 10 verified citations
Verdict: ALREADY_SHIFTED
Language Horizontal Gene Transfer
Full article (4,985 chars). 10 sources. Bayesian AUC: 0.32. Uncertainty: 0.34. Passed ALL gates.
Sources: 10 · Bayesian AUC: 0.32
Verdict: 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. Claude, Cursor, Cline, Continue.dev.
c4_solve
12-stage discovery pipeline
c4_search
47 configured 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 bridges
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
ASCII cube. Gradient bars. Spark particles. Night mode. The terminal is not a fallback — it is the primary interface.
Planned Integrations
CESM and JuliaDiff are on the roadmap. Targeted for v5.6+.
CESM — Earth System
Community Earth System Model for climate simulation. Full atmospheric, ocean, land, and sea-ice coupling.
JuliaDiff — Auto-Diff
Automatic differentiation in Julia. Forward and reverse mode for scientific machine learning (SciML).
Hardened for Production
0 CRITICAL. 0 HIGH. 222 fixes across 4 audit rounds.
Prompt Injection
Nonce delimiters + LaTeX escaping + HTML entity decoding. Fail-closed.
SSRF Protection
Paper ID validation. Redirects disabled. Confined to ~/.c4reqber.
Subprocess Hardening
Shell metacharacter blocking. Symlink guards. Path traversal blocked.
Auth
JWT + HMAC. Dev-mode bypass with token. No secrets in code.
3 Commands to Discovery
# 1. Install
pip install c4reqber
# 2. Set your key
export OPENROUTER_API_KEY=sk-or-...
# 3. Run
c4reqber "quantum biology in photosynthesis"
# → paradigm-shifting hypothesis + dissertation + citations
# Model-per-stage config
c4reqber config --tier budget --save # $0.002/pipeline
c4reqber config --tier premium --save # Claude Opus everywhere
c4reqber config --set D=gemma4:26b # Local model for hypotheses
Academic tip: Run with --verify flag to auto-invoke Lean4/Coq for theorem-checking.
What Is Next
Continuous delivery of simulation engines, AI integrations, and verification backends.
59 Scientific Computing Engines
5 internal GPU engines + 31 open-source bridges + 23 planned integrations. From molecular dynamics to climate modeling.
| Domain | Engine | Description | Status |
|---|---|---|---|
| Physics | Newton | Classical mechanics, N-body, orbital | Built-in GPU |
| Physics | JaxSim | Differentiable physics, robotics | Built-in GPU |
| Physics | TorchSim | PyTorch-native material simulation | Built-in GPU |
| Physics | OpenFOAM | CFD, turbulence, multiphase | P1 Bridge |
| Physics | Elmer FEM | Multiphysics FEM solver | P1 Bridge |
| Chemistry | PySCF | Quantum chemistry, DFT | P1 Bridge |
| Chemistry | RDKit | Cheminformatics, SMILES | P1 Bridge |
| Chemistry | Open Babel | Molecular format conversion | P1 Bridge |
| Bio | GROMACS | Molecular dynamics | P1 Bridge |
| Bio | NEURON | Neuronal simulation | P1 Bridge |
| Bio | Brian2 | Spiking neural networks | P1 Bridge |
| Bio | Virtual Bio | GPU-accelerated bio pipeline | Built-in GPU |
| Climate | WRF | Weather research & forecasting | P1 Bridge |
| Stats | Stan | Bayesian inference | P1 Bridge |
| Stats | PyMC | Probabilistic programming | P1 Bridge |
| ML | ONNX Runtime | Cross-platform inference | Built-in |
| ML | MLX | Apple Silicon ML | Built-in GPU |
| Math | SciPy | Scientific computing | Built-in |
P1 = Python-native open-source bridge available now · Planned = on roadmap · Full list in simulation_engines_report.md
47 Knowledge Sources — Real Citations
No hallucinated references. Every citation is verified against live databases with DOI.
9 Formal Verification Backends
Your hypotheses don't just claim — they prove. Auto-selected by domain.
Lean4
Dependent type theory for mathematics
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
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
| RAM | 4 GB (8 GB rec) |
|---|---|
| CPU | 2 cores (4+ for sim) |
| Disk | 2 GB + engines separately |
| GPU | Optional · Apple Silicon / CUDA |
Note: pip install c4reqber installs the Python package + CLI only. External simulation engines (GROMACS, OpenFOAM, etc.) require separate installation per engine. See GPU_SETUP.md.
5 Cost Tiers
From $0.002 to $0.11 per full pipeline run. Configure per phase.
Social Publishing — 9 Platforms
Dissertation → LaTeX + BibTeX → Auto-upload → ORCID → Social blast.
Workflow: Dissertation → LaTeX + BibTeX → Auto-upload → ORCID registration → Social blast