1. A computer system for recommending an optimal treatment protocol comprising: a model of biological processes related to a disease; a treatment protocol generator for generating a plurality of treatment protocols for treating a disease using drugs; and a selector adapted to select an optimal treatment protocol from said plurality of treatment protocols based on the model the model further comprising: a pharmacokinetics macro module adapted to analyze interactions between a ligand and a population of target cells at a tissue level; a pharmacokinetics micro module adapted to analyze interactions between the ligand and a cell at an individual cell level; the micro module adapted to model behavior of the ligand and receptors related to single cell level of ligand-cell interactions, as a stochastic process.