A method has been developed for using genome-wide transcription profile (i.e., gene-expression level) values to derive a gene expression index used as a kinetic value for every biological reaction and process assigned to each and every gene. This kinetic value is used in computational biology programs, i.e., mathematical models integrating genome, transcriptome, proteome, reactome, fluxome, metabolome, physiome, and phenome, in any combination, for simulations or theoretical systematic analyses of all life forms. This approach allows a model to be generated for any individual organism at any state of life, health condition, or disease/traumatic process. The model can include any or all biological reactions and processes, because an exact kinetic value becomes available; and, thereby, the outcomes represent stable or dynamic states of the individual organism at the time the biological specimen or sample was collected. Model systems without and with regulatory steps and mechanisms can be used to assess the pres
