Bio-binaries v0.2.1
33 bio-inspired system utilities — Binary protocol orchestration, quantum-space simulation, machine-brain inference.
A modular ecosystem where each command represents a biological principle: viral infection, plasmid injection, neural synchronization, resonance fields, homeostasis. Pure Rust, 100% binary protocol.
viral-infect
— infection cascade, signal propagationhox-diff
— differential activation, gene expressionplasmid-dream
— dream sequence generationplasmid-inject
— vector delivery systemmutation-sentinel
— file mutation monitoring
telepathy-sync
— entanglement synchronizationtelepathy-entangle
— quantum correlationeqm-pulse
— electromagnetic pulse shapingeqm-methy
— methylation state encodinggrid-warp
— spatial distortion fieldspath-resonance
— resonance path findingaether-fabric
— topological field mappingaether-excite
— quantum field excitation
borg-cube
— collective consciousness nodebrain-synapse
— synaptic connection modelingbrain-connectome
— connectome reconstructioncollective-sync
— hive mind synchronizationnexus-logic
— logic gate fusionmicroscope-mem
— memory layer interfaceribosome-synth
— protein synthesis (binary mitosis)vagus-nerve
— internal organ sensing (CPU/RAM → WaveField)
wave-encoder
— wave pattern encoding (432 Hz base)wave-sculptor
— wave shaping filter (DSP)wave-field
— self-organizing interference fieldiron-resonate
— iron-core resonance profilingmagneto-acoustic
— acoustic-magnetic coupling (code → audio)magneto-geo
— geomagnetic field interaction (code heatmap)mycelium-spread
— fungal network propagation (filesystem mapping)homeostasis
— system equilibrium maintenance
omega-master
— Queen orchestrator (central server)omega-point
— singularity convergence detectorwave-cryo-tx
— acoustic cryo-transmitter (BFSK modem)wave-cryo-rx
— acoustic cryo-receiver (BFSK demodulation)
| Binary | Layer | Description | Status |
|---|---|---|---|
omega-master |
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| Control | Queen orchestrator — drone registration, task dispatch, BioMessage protocol | ✅ | |
omega-point |
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| Control | Convergence detector — system coherence monitoring | ✅ | |
viral-infect |
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| Bio-Evolution | Regex-based code transformation at scale | ✅ | |
hox-diff |
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| Bio-Evolution | Project structure differentiator | ✅ | |
plasmid-dream |
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| Bio-Evolution | Predictive error analyzer — build runner + trend analysis | ✅ | |
plasmid-inject |
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| Bio-Evolution | Surgical file patching at line level | ✅ | |
mutation-sentinel |
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| Bio-Evolution | File mutation watcher — auto-freeze on changes | ✅ | |
telepathy-sync |
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| Quantum-Space | BLAKE3 delta directory synchronization | ✅ | |
telepathy-entangle |
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| Quantum-Space | Inter-process shared state via temp files | ✅ | |
eqm-pulse |
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| Quantum-Space | System health monitor + FFT frequency analysis | ✅ | |
eqm-methy |
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| Quantum-Space | File consolidator — BLAKE3 integrity index with methylation rate | ✅ | |
aether-excite |
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| Quantum-Space | Resource excitation monitor — per-region system load | ✅ | |
aether-fabric |
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| Quantum-Space | System topology mapper — process/port/connection graph | ✅ | |
borg-cube |
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| Machine-Brain | Parallel command replicator — exponential scaling | ✅ | |
brain-synapse |
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| Machine-Brain | File co-change tracker — Hebbian git analysis | ✅ | |
brain-connectome |
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| Machine-Brain | Dependency graph builder — static import analysis | ✅ | |
collective-sync |
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| Machine-Brain | Multi-process state reconciliation — distributed consensus | ✅ | |
nexus-logic |
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| Machine-Brain | Knowledge indexer — local full-text trigram search engine | ✅ | |
ribosome-synth |
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| Machine-Brain | Code generator & self-replicator — binary mitosis engine | ✅ | |
microscope-mem |
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| Machine-Brain | Memory layer interface (Microscope API compatibility) | ✅ | |
vagus-nerve |
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| Machine-Brain | Internal organ sensing — CPU/RAM → WaveField | ✅ | |
wave-encoder |
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| Resonance | Data→wave encoder — FFT-based file encoding (432 Hz base) | ✅ | |
wave-sculptor |
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| Resonance | Frequency filter — digital signal processing on wave packets | ✅ | |
wave-field |
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| Resonance | Self-organizing wave interference field | ✅ | |
iron-resonate |
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| Resonance | Hardware resonance monitor — HW performance profiler | ✅ | |
path-resonance |
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| Resonance | Hot-path detector — filesystem activity heatmap | ✅ | |
grid-warp |
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| Resonance | Symlink/junction manager + latency measurement | ✅ | |
magneto-geo |
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| Resonance | Error hotspot detector — code quality heatmap scanner | ✅ | |
magneto-acoustic |
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| Resonance | Code health sonifier — error patterns to audio (WAV) | ✅ | |
mycelium-spread |
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| Resonance | Recursive filesystem mapper — network graph builder | ✅ | |
homeostasis |
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| Resonance | System equilibrium maintenance | ✅ | |
wave-cryo-tx |
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| Audio | Acoustic CryoFrame transmitter — BFSK modulated WAV output | ✅ | |
wave-cryo-rx |
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| Audio | Acoustic CryoFrame receiver — BFSK demodulation from WAV | ✅ |
v2 BioMessage (Primary — 100% binary)
- Header: 60 bytes (BLAKE3 auth, nonce replay protection)
- Payload: TLV-style field encoding
- 22 opcodes: JOIN, TASK, RESULT, HEARTBEAT, CLONE, GENOME, APOPTOSIS, FREEZE, THAW, CRISPR_PATCH, IMMUNE_ALERT, HOMEO_SYNC, MICRO_QUERY, and more
- Drones use
bio_client::DroneClient
over UDP - Stateless, concurrent, replay-protected via NonceWindow
v1 Echo-X (Legacy — deprecated)
| Module | Format | Purpose |
|---|---|---|
| wave_store | Custom TLV | Wave packet archive |
| cryo | bincode + zlib | Cryogenic snapshots (FFT spectral state) |
| microscope_mem | bincode index | Memory layer |
| eqm_methy | bincode | Methylation state |
| telepathy_entangle | bincode | Entanglement records |
No JSON in production storage. External APIs (Ollama, dream_loop) use JSON as bridge only.
cargo check
cargo build --release
./target/release/omega-master status
./target/release/omega-master start --listen 127.0.0.1:8888
ls target/release/*.exe | grep -v deps | sed 's|target/release/||;s|\.exe$||'
| Module | Lines | Description |
|---|---|---|
bio_protocol.rs |
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| 553 | Binary protocol: encode/decode, TLV fields, CRC64, replay protection | |
cryo.rs |
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| 867 | FFT-based spectral snapshots (CryoFrame), freeze/thaw engine | |
acoustic.rs |
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| 675 | BFSK modem: Goertzel demodulation, hand-written WAV I/O | |
auth.rs |
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| 253 | QueenKey (BLAKE3 keyed), DroneToken, BinaryIntegrity gate macro | |
bio_client.rs |
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| 63 | UDP DroneClient: JOIN, heartbeat, result send | |
system.rs |
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| 129 | sysinfo-based system snapshot (CPU, RAM, disk, processes) | |
omega_master.rs |
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| 667 | Queen orchestrator: drone registry, task dispatch, CLI |
Project stats: ~17,300 lines of Rust, 92 source files, 33 binary targets.
sysinfo = "0.30" # System info
blake3 = "1.5" # BLAKE3 hashing
clap = "4" # CLI parsing
serde = "1.0" # Serialization
bincode = "1.3" # Binary encoding
serde_json = "1.0" # JSON (external APIs only)
tokio = "1" # Async runtime
colored = "2" # Terminal colors
memmap2 = "0.9" # Memory mapping
chrono = "0.4" # Timestamps
notify = "6" # File watching
rustfft = "6" # FFT spectral analysis
flate2 = "1.0" # Zlib compression
qrcode = "0.14" # QR code generation
reqwest = "0.13.2" # HTTP (external API bridge)
src/
├── lib.rs # Module declarations
├── commands/ # 33 command modules
│ ├── mod.rs
│ ├── omega_master.rs # Queen orchestrator
│ ├── viral_infect.rs # Code transformer
│ ├── telepathy_sync.rs # Delta sync
│ ├── ... # 30 more command modules
├── bin/ # 33 binary entry points
│ ├── omega_master.rs
│ ├── viral_infect.rs
│ └── ... # 31 more entry points
├── bio_protocol.rs # v2 BioMessage format
├── bio_client.rs # Drone client protocol
├── auth.rs # BLAKE3 authentication
├── cryo.rs # Cryogenic snapshots (FFT)
├── acoustic.rs # BFSK modem
├── wave_store.rs # Wave packet storage
├── system.rs # System monitoring
├── wave_field.rs # Wave field simulation
├── magneto.rs # Magnetic field utilities
├── mitosis.rs # Binary replication
├── leash.rs # Metabolic token management
└── ...
Cargo.toml # Dependencies & metadata
Cargo.lock # Locked versions
Binary Integrity Check— BLAKE3 self-hash at startup; if the binary changed since last verified run, exits with code 77** Queen Key Authentication**— Ed25519-style BLAKE3 keypair, drone session tokens (1-hour expiry)** Nonce Replay Protection**— rolling window of seen nonces in BioMessage protocol** CRC64 Checksums**— every BioMessage has a checksum covering header + payload** Exponential Power Limit**— borg-cube caps at 2^N (typical: 2^4 = 16) to prevent DoS** CRC-16 CCITT**— acoustic frames have CRC-16 error detection** Constant-Time Comparison**— auth tag verification is timing-safe
Máté Róbert (Silent) — bio-binaries orchestration system
A research project exploring bio-inspired computing principles through a pure Rust ecosystem. Each module represents a biological metaphor: viral propagation, quantum entanglement, neural connectivity, resonance fields, homeostatic balance.
Not a toy. Deployment-ready code.
cargo check
cargo run --release --bin omega-master -- status
cargo run --release --bin viral-infect -- . --pattern "TODO" --replace "DONE" --dry-run
cargo run --release --bin wave-cryo-tx -- test
cargo run --release --bin cryo-freeze
Status: 🎯 Ready for deployment — All 33 binaries compile and run, binary protocol verified.
Last verified: 2026-06-03 | Cargo check: 0 errors