With near 11,500 genome sequencing projects around the world, the availability of the tremendous amount of whole genome sequences has no doubt opened up new avenues for genome-wide innovative research. By analyzing the whole genome information for similarities/differences, it has become possible to identify new genomic codes and their global roles. Our group is interested in applying both reverse and forward engineering approaches to characterize genome structures in natural living cells and investigating their use in forward genome design and engineering. A key aim of synthetic genomics research is to be able to use the knowledge obtained through systems biology and to design and construct whole genomes for pursuing genome-scale biology. Two factors are apparently critical to the success of synthetic genome projects. First is the information on functional organization of the biological molecules and their interactions within a living cell. Second is a comprehensive infrastructure for executing genome-scale design process from conception to final output of blueprints. Towards these demands, our team has applied engineering principles to the design and construction of complex biological systems. In this talk, I will present our GenomeCAA and GenomeCAD - Computer Aided Analysis and Design of Microbial Whole Genomes. We provide whole genome analysis and design solutions to capture and to understand the underlying mechanisms behind multi-level and multi-scale high-throughput experimental data of various microorganisms.