E-CELL project: Towards integrative simulation of cellular processes

A general framework for modeling gene expression using the E-CELL system is presented. Using the framework, the following three gene regulation systems: the lac operon and the araBAD operon of E. coli, and the lytic-lysogenic switch network in bacteriophage λ, are modelled and simulated. E-CELL simulates the behavior of model cell by computing interactions among molecular species it contains and allows the user to define chemically discrete compartments such as membranes, chromosomes, and cytoplasm. A detailed model of the gene expression process as a part of the self-supporting cell model is constructed. To simulate complex gene regulation systems with a large number of genes, a more abstract and simpler model is desired for the sake of efficiency.