The present invention provides methods and accompanying computer-based systems and computer-executable code stored on a computer-readable medium for constructing a model of a biological network. The invention further provides methods for performing sensitivity analysis on a biological network and for identifying major regulators of species in the network and of the network as a whole. In addition, the invention provides methods for identifying targets of a perturbation such as that resulting from exposure to a compound or an environmental change. The invention further provides methods for identifying phenotypic mediators that contribute to differences in phenotypes of biological systems.
 This invention was made with Government Support under Contract Number F30602-01-2-0579, awarded by the Air Force Research Laboratory, Grant Number EIA-0130331 awarded by the National Science Foundation, Grant Number N00014-99-1-0554 awarded by the Office of Naval Research, and Grant Number DE-FG02-04ER63803 awarded by the Department of Energy. The Government has certain rights in the invention.