Bio

Biological computing interfaces: DNA-based weight storage, gene regulatory network modulation, and neuromodulatory dynamics (dopamine, serotonin, norepinephrine).

DNAEncoder — DNA Data Storage

Maps bitstreams to nucleotide sequences and back. Encoding: pairs of bits → nucleotides (00→A, 01→C, 10→G, 11→T). Decoding includes a configurable mutation rate that simulates sequencing errors.

Parameter	Default	Meaning
mutation_rate	0.001	Per-nucleotide mutation probability during decode

Odd-length bitstreams are zero-padded to even length.

GeneticRegulatoryLayer — Gene Expression Modulation

Neural activity drives protein production; protein levels modulate neuron thresholds. Implements a first-order ODE: dP/dt = α * spikes - β * P, clipped to [0, 10].

Parameter	Default	Meaning
n_neurons	(required)	Number of neurons
production_rate	0.01	Protein production rate (α)
decay_rate	0.005	Protein decay rate (β)

get_threshold_modulators() returns current protein levels — higher protein → higher effective threshold (inhibitory feedback).

NeuromodulatorSystem — Global Emotional System

Three neuromodulators with environmental feedback:

Chemical	Baseline	Effect
Dopamine (DA)	0.5	Lowers threshold (excitation)
Serotonin (5-HT)	0.5	Reduces noise (stabilization)
Norepinephrine (NE)	0.1	Increases noise + gain (exploration)

update_levels(reward, stress) adjusts chemicals. modulate_neuron(params) returns modified parameters.

Usage

from sc_neurocore.bio import DNAEncoder, GeneticRegulatoryLayer, NeuromodulatorSystem
import numpy as np

# DNA storage roundtrip
enc = DNAEncoder(mutation_rate=0.0)
bits = np.array([1, 0, 0, 1, 1, 1, 0, 0], dtype=np.uint8)
dna = enc.encode(bits)   # "GCTA"
recovered = enc.decode(dna)
assert np.array_equal(bits, recovered)

# Gene regulation
grn = GeneticRegulatoryLayer(n_neurons=100)
for _ in range(50):
    spikes = (np.random.rand(100) < 0.3).astype(float)
    grn.step(spikes)
thresholds = grn.get_threshold_modulators()

# Neuromodulation
nm = NeuromodulatorSystem()
nm.update_levels(reward=0.8, stress=0.2)
params = nm.modulate_neuron({"v_threshold": 1.0, "noise_std": 0.1})

::: sc_neurocore.bio.dna_storage options: show_root_heading: true

::: sc_neurocore.bio.grn options: show_root_heading: true

::: sc_neurocore.bio.neuromodulation options: show_root_heading: true