Synthetic Genome Design for Biomanufacturing: Integrated Modeling with CRISPR Tools, Python, and Geneious

Abstract: This study presents a comprehensive approach to synthetic genome design aimed at enhancing microbial biomanufacturing performance. The framework integrates CRISPR-based gene editing (using CHOPCHOP), sequence assembly with Geneious, and metabolic pathway modeling using Python's COBRApy library. We simulate and validate biofuel yield under varying fermentation conditions and quantify transcriptomic changes induced by genome editing. Statistical analysis reveals the optimal design parameters for scalable biofuel production and gene expression stability. Keywords: CRISPR, Biomanufacturing, Synthetic Biology, Geneious, COBRApy, Genome Editing, Transcriptomics, Biofuel Yield, Gene Expression