Other computer models of the cell are being developed, but they often try to reproduce individual cellular processes in detail. Biochemistry simulated by E-CELL Software. Written to run under the UNIX or Linux operating systems, the software relies on the user to input a cell's molecules, their locations and estimated concentrations within the cell, and the reaction rules that govern them. E-CELL then computes how the abundance of each substance at a particular location changes at each time increment. With a single mouse click, the user can knock out particular genes or groups of related genes, expose the cell to a foreign substance or deprive it of a nutrient, and then run the simulation again.
Graphical interfaces allow the user to monitor the cell's changing chemistry.
Most of the genes were based on those of Mycoplasma genitalium , a microbe that has the smallest known gene set of any self-replicating organism. But the genes for some vital cellular processes still have not been identified in the mycoplasma, so the group added genes from other organisms. This bare-bones cell has already delivered one surprise. But unexpectedly, before ATP levels drop they briefly rise. Cutting the supply of glucose shuts down the early stages of the pathway, stopping ATP consumption there even while ATP continues to be produced from intermediary metabolites further down the pathway.