Since we completed the sequencing of E. coli in early 1997, we have designed and constructed a genome database of this organism, GenoBase. As a world-leader in functional analysis of genomes in the post-sequencing era, it is time to face the next mission of genome analysis, i.e. metabolome analysis. Our objectives are the quantitative modeling of a cell, particularly focusing on 1) complete elucidation of pathways by gene deletion, 2) metabolite flow in a cell, 3) parameters of each enzyme involved in the pathway, 4) gene network analysis, and 5) construction of protein-protein interaction maps. Through these analyses, we aim for the thorough understanding of a cell, enough to construct a virtual E. coli within a computer. Our research is applicable to other organisms valuable to human.