bio-logic-compiler 0.1.0

A Python MVP for a Bio-Logic Compiler that models neural circuits as graphs, analyzes neuron firing thresholds, and reverse-engineers Boolean logic gates from biological connectivity.

Bio-Logic Compiler

This project provides a Python MVP for a Bio-Logic Compiler that models neural circuits as graphs, analyzes neuron firing thresholds, and reverse-engineers Boolean logic gates (AND, OR, NOT, NAND, NOR, etc) from biological connectivity.

Features

• Model neurons as nodes and synapses as weighted edges (networkx)
• Add synapses manually or ingest from JSON/CSV files
• Extract logic gates from neuron thresholds and synaptic weights
• Detects AND, OR, NOT, NAND, NOR, direct pass-through, and complex motifs
• Visualize neural circuits with matplotlib
• Comprehensive unit tests

Usage

1. Install dependencies

   pip install -r requirements.txt
   

2. Run Example

   python bio_compiler.py
   

   python -m unittest test_bio_compiler.py
   

   python test_visualization.py
   

File Structure

• bio_compiler.py — Main class and logic extraction
• app.py — Dash web app (main UI)
• sample_circuit.json / sample_circuit.csv — Example data
• requirements.txt — Dependencies
• pyproject.toml, setup.py — Packaging

Logic Extraction Principle

A neuron fires if:

$$ \sum (I_n \cdot w_n) \geq \theta $$

Where $I$ is the input (0 or 1), $w$ is the synaptic weight, and $\theta$ is the threshold.

• AND: All excitatory inputs must be active (threshold = sum of weights)
• OR: Any excitatory input triggers firing (threshold <= min weight)
• NOT: Inhibitory input vetoes firing
• NAND/NOR: Mixed motifs with both excitatory and inhibitory inputs

Extending

• Add support for temporal summation and motif discovery
• Integrate with real connectome data (e.g., FlyWire)
• Enhance visualization and reporting

Advanced Features

• FlyWire connectome data ingestion (JSON/CSV)
• Temporal modeling (simulate time steps)
• Motif discovery (logic motif extraction)

Packaging

• pyproject.toml and setup.py for pip/Poetry installation
• requirements.txt for quick dependency install

License

MIT