synthetic-biology

name	synthetic-biology
description	Engineering biological systems
license	MIT
compatibility	opencode
metadata	{"audience":"synthetic biologists, engineers, researchers","category":"biology"}

What I do

• Design and construct new biological parts
• Engineer metabolic pathways
• Create synthetic gene circuits
• Develop biosensors and therapeutics
• Program cells with new functions
• Apply design-build-test-learn cycles

When to use me

• When engineering new biological functions
• When designing gene circuits
• When creating metabolic pathways
• When developing biosensors
• When programming cells
• When building synthetic organisms

Key Concepts

Design Principles

Standardization

• BioBricks: Standardized parts
• RFC standards: Assembly rules
• SBOL: Data exchange format

Genetic Circuits

# Example: Toggle switch design
class ToggleSwitch:
    """
    Bistable genetic switch.
    """
    def __init__(self):
        self.components = {
            'promoter1': 'Repressor 1',
            'promoter2': 'Repressor 2',
            'repressor1': 'Inhibits promoter2',
            'repressor2': 'Inhibits promoter1'
        }
    
    def states(self):
        return {
            'state_A': 'Repressor1 ON, Repressor2 OFF',
            'state_B': 'Repressor1 OFF, Repressor2 ON'
        }

# Circuit types
circuit_types = {
    'inverter': 'NOT gate',
    'amplifier': 'Signal enhancement',
    'oscillator': 'Repressible gene expression',
    'memory': 'State persistence',
    'logic_gates': 'AND, OR, NAND, NOR'
}

Metabolic Engineering

• Pathway design
• Cofactor balancing
• Flux optimization
• Enzyme engineering
• Compartmentalization

Applications

• Biofuels production
• Pharmaceutical synthesis
• Bioremediation
• Biosensors
• Therapeutic cells
• Living materials