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synthetic-biology

Synthetic biology design and simulation tools. Codon optimization, gene circuit ODE modeling with growth feedback, SBML model creation, bifurcation analysis, barcode sequencing fitness analysis, and therapeutic genome engineering. For metabolic modeling use cobrapy; for sequence tools use biopython.

backend/cli/skills/biology/synthetic-biology/SKILL.md

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# Synthetic Biology: Design & Simulation

## Overview

Synthetic Biology provides computational tools for designing and simulating engineered biological systems. This skill covers codon optimization with species-specific usage tables, gene circuit ODE modeling (repressilator, toggle switch, inducible promoters) with growth dilution coupling, SBML model creation and validation using python-libsbml, bifurcation analysis for bistable circuits, barcode sequencing fitness analysis, and genome engineering with expression cassette insertion. All simulations produce quantitative outputs suitable for guiding experimental design.

## When to Use This Skill

- Optimizing gene sequences for heterologous expression (codon adaptation)
- Simulating gene circuit dynamics (toggle switches, repressilators, inducible systems)
- Creating standardized SBML models of biological networks
- Analyzing bistability and bifurcation behavior in synthetic circuits
- Processing barcode sequencing data for fitness landscape analysis
- Designing expression cassettes and generating annotated plasmid maps