c4reqber
The cognitive exoskeleton for humans and AI agents.
Think. Simulate. Prove. Discover.
SHIFT PARADIGMS
What is c4reqber?
In plain language — no jargon required.
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.
Install
One command. Python 3.11+. Bring your own API key (OpenRouter, Mistral, etc.). Optional GPU for heavy sims.
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.
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.
Formal Verification Engine
Lean4, Coq, Dafny, Agda, Z3, Hoare logic — your hypotheses don't just claim, they prove.
38 Simulation Engines
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, Materials Project, Kaggle, OpenFDA, ORCID, and other configured sources. MultiSourceSearcher with circuit breaker and semantic dedup.
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).
MCP Server — 21 Tools
Expose full C4REQBER capability to AI agents. JSON Schema compliant. stdio JSON-RPC.
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.
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.
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 | C4-META | SOAR | ACT-R | GWT | IIT | PMCSF | ConSpaces | Freud | Plato |
|---|---|---|---|---|---|---|---|---|---|
| Dimensions | 3 (Z₃) | 2 | 2 | 1 | N | 17 | 3 | 3 | 3 |
| States | 27 (discrete) | Symbolic | Chunks | Broadcast | Φ | Continuous | Regions | Psychoanal. | Forms |
| Representation | Discrete (Z₃³) | Symbolic (rules) | Symbolic (chunks) | Continuous (broadcast) | Continuous (Φ) | Continuous (17D vectors) | Geometric (regions) | Psychoanalytic | Dialectical (forms) |
| Formalism | Group theory | Production | Production | Descriptive | Info. theory | Vectors | Geometry | Clinical | Philosophy |
| Verification | Lean4 + Coq | No | No | No | No | No | No | No | No |
| Navigation | Theorem 9 | Rules | Rules | No | No | Gradient | Paths | No | No |
| Reachability | Theorem 11 | No | No | No | No | No | No | No | No |
| Cross-Domain | Universal | AI only | Cognitive | Conscious. | Conscious. | NLP only | Spatial | No | No |
| Open Source | AGPL-3.0 | BSD | BSD | No | No | No | MIT | No | No |
| 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 | c4reqber | Elicit | Consensus | Scite.ai | Perplexity | ChatGPT DR | Gemini DR | Semantic Scholar | GNoME | A-Lab | AlphaFold3 | Insilico | Recursion | Schrödinger | Cradle | AI Scientist | OpenAlex | Lean4+AI | Dafny+AI | Neo4j+KG | COMSOL+AI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Lit. Review | ● | ● | ● | ● | ● | ● | ● | ● | ◐ | ◐ | ◐ | ◐ | ◐ | ◐ | ◐ | ◐ | ● | ○ | ○ | ◐ | ○ |
| Hypothesis | ● | ◐ | ◐ | ◐ | ◐ | ● | ● | ◐ | ◐ | ◐ | ◐ | ● | ● | ◐ | ◐ | ● | ○ | ○ | ○ | ◐ | ○ |
| Simulation | ● | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ● | ● | ● | ● | ● | ● | ● | ◐ | ○ | ○ | ○ | ○ | ● |
| Formal Verify | ● | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ● | ● | ○ | ○ |
| Multi-Domain | ● | ○ | ○ | ○ | ◐ | ● | ● | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ◐ | ○ | ○ | ○ | ○ | ◐ | ○ |
| Auto Publish | ● | ◐ | ◐ | ◐ | ◐ | ● | ● | ◐ | ◐ | ◐ | ◐ | ◐ | ◐ | ◐ | ◐ | ● | ○ | ○ | ○ | ◐ | ◐ |
| WASM Runtime | ● | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ |
| MCP Server | ● | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ○ | ◐ | ○ | ○ |
| Open Source | AGPL-3.0 | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | ◐ | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | ✕ | ● | ● | ● | ◐ | ◐ | ✕ |
| Price | Free (BYOK) | $29-49/m | $7-49/m | $20-79/m | $20/m | $20-200/m | Plan | Free | Free | Research | Free/Comm | Enterprise | Enterprise | Enterprise | Enterprise | Free | Free | Free | Free | Enterprise | Enterprise |
● 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.
| Product | Actual scope | Where it leads | Limits versus c4reqber |
|---|---|---|---|
| Claude Science | Paid 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‑Rosalind | Controlled-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. |
| Prism | Free 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.
| 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 |
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
Real Export Formats
Production-ready outputs generated by the actual pipeline.
Check examples
F⟨Past,Concrete,Self⟩ → tau- → lambda- → kappa-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
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.
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.
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.
| 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 | NVIDIA | Native CUDA kernels (cuBLAS, cuDNN) | Built-in GPU |
| Physics | Schr | Quantum electrodynamics solver | P1 Bridge |
| Physics | FEniCSx | Finite element method PDE solver | P1 Bridge |
| Physics | OpenFOAM | CFD, turbulence, multiphase | P1 Bridge |
| Chemistry | PySCF | Quantum chemistry, DFT | P1 Bridge |
| Chemistry | Psi4 | Ab initio quantum chemistry | P1 Bridge |
| Chemistry | Quantum ESPRESSO | Plane-wave DFT | P1 Bridge |
| Chemistry | LAMMPS | Large-scale atomic/molecular MD | P1 Bridge |
| Chemistry | GROMACS | Molecular dynamics | P1 Bridge |
| Chemistry | Vina | Protein-ligand docking | P1 Bridge |
| Bio | OpenMM | GPU molecular dynamics, protein folding | Built-in GPU |
| Bio | NEURON | Biophysical neuron simulation | P1 Bridge |
| Bio | Brian2 | Spiking neural networks | P1 Bridge |
| Bio | Jaxley | Differentiable biophysical neurons | P1 Bridge |
| Bio | Tellurium | Systems biology simulation | P1 Bridge |
| Bio | COPASI | Biochemical network simulation | P1 Bridge |
| Bio | MDAnalysis | MD trajectory analysis | P1 Bridge |
| Bio | BoolNet | Gene regulatory networks | P1 Bridge |
| Bio | Cobra | Metabolic flux analysis | P1 Bridge |
| Bio | SLiM | Population genetics simulation | P1 Bridge |
| Climate | WRF | Weather research & forecasting | P1 Bridge |
| Climate | Xarray | Climate data analysis | P1 Bridge |
| Astronomy | AMUSE | Astrophysics multiphysics framework | P1 Bridge |
| Astronomy | Rebound | Planetary dynamics N-body | P1 Bridge |
| Robotics | MuJoCo | Contact dynamics simulator | P1 Bridge |
| Robotics | PyBullet | Robotics simulation engine | P1 Bridge |
| Math & Stats | DiffEqPy | ODE/PDE solver suite | P1 Bridge |
| Math & Stats | ModelingToolkit | Symbolic modeling and simulation | P1 Bridge |
| Math & Stats | JAX-LAB | Lattice Boltzmann method | P1 Bridge |
| Math & Stats | Taichi | GPU simulation framework | P1 Bridge |
| Math & Stats | Mesa | Agent-based modeling framework | P1 Bridge |
| Math & Stats | SimPy | Discrete event simulation | P1 Bridge |
| Math & Stats | JAX-MD | Differentiable molecular dynamics | P1 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 keyExa.ai
Neural search · Semantic
API keyTavily
AI search · Academic focus
API keySemantic Scholar
Academic · 200M+ papers
FreeCORE
Open access · 10M+ full-text
API keyBASE
Academic · 150M+ docs
API keyOA.mg
Open access · 250M+ papers
API keyUnpaywall
OA articles · 40M+ records
API keyLens.org
Scholarly + patents · 225M+
API keyResearch Databases
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
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
| RAM | 4 GB (8 GB rec) |
|---|---|
| CPU | 2 cores (4+ for sim) |
| Disk | 2 GB + engines separately |
| GPU | Optional · 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.
What Is Next
Continuous delivery of simulation engines, AI integrations, and verification backends.
Social Publishing — Multi-Channel
Discovery → draft → blast social publish. Zenodo DOI + every configured social channel (skipped if no API key).
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, publishCLI:
blast social publish·blast social post --id … --platform mastodonFull guide: docs/SOCIAL_PUBLISHING.md on GitLab