IBM and NeSC workshop on Protein Science

E-CELL: Towards integrative modeling of cellular processes

M. Tomita

E-CELL Project (http://www.e-cell.org) was launched in 1996 at Keio University in order to model and simulate various cellular processes with the ultimate goal of simulating the cell as a whole. E-CELL System, a generic software package we have developed, enables us to model not only metabolic pathways but also other higher-order cellular processes such as protein synthesis and signal transduction. 

Using the system, we have successfully constructed a virtual cell with 127 genes sufficient for ``self-support''.  The gene set was selected from the genome of Mycoplasma genitalium, and the metabolisms include transcription, translation, membrane transport, the glycolysis pathway for energy production, and the phospholipid biosynthesis pathway for membrane structure. Since all its proteins and membrane structure are modeled to degrade spontaneously over time, the virtual cell must keep synthesizing proteins and phospholipid bilayer to sustain its life.  It thus uptakes glucose as its energy source, and emptying glucose in the environment would result in “cell death from hunger”. 

  Modeling Group in our institute is now developing many different models of cellular processes, including bacterial chemotaxis, circadian rhythms, photosynthesis, as well as cell cycle and cell division. For organelles, a quantitative model of mitochondria is nearly complete, and we will be soon developing chloroplasts in the context of e-Rice Project funded by Japanese ministry of agriculture. For human cells, we have already developed a quantitative model of erythrocytes, and being used in pathological analyses of enzyme deficiencies causing anemia. Other human cells now being developed include myocardial cells, neural cells, and pancreatic beta-cells.