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The use of mathematical modeling te chniques in biomedical research is playing an increasingly important role aso ne seeks tounderstand the physiopathology of disease processes. This includes not only understand ing mechanisms ofphysiological processes, but diagnosis and treatment. In addition, its introduction in the study of genomics andproteomics is key in understanding the functional ch aracteristics of gene expression and protein assembly and secretion. Finally, with the increasing com plexity and associated cost of drug development, modeling techniques are being used to streamline the process. We have workedin c lose collaboration with colleagues in biomedical and pharmaceutical research for a number of years applying and refining mathematical modeling techniques to avariety o f problems. In addition, we haveworked incollaboration with colleagues in applied m athematics and statistics to develop new algorithms to solve new setsof problems as theyemerge ino ur research efforts. Finally, we have worked with colleagues in computer sciencet o develop new software tools that bring the power of mathematical modeling to a broad research community. This books brings together mucho f what we have learned over the years, and presents the material in a format that should be accessible both to the novice reader and those desiring more detailed information about specific techniques.