AutoAnalyze is a highly customizable framework for the visualization and analysis of large-scale model graphs. Originally developed for use in the automotive domain, it also supports efficient computation within molecular networks represented by reaction equations. A static analysis approach is used for efficient treatment-condition-specific simulation. The chosen method relies on the computation of a global network data-flow resulting from the evaluation of individual genetic data. The approach facilitates complex analyses of biological components from a molecular network under specific therapeutic perturbations, as demonstrated in a case study. In addition to simulating the complex networks in a stable and reproducible way, kinetic constants can also be fine-tuned using a genetic algorithm and built-in statistical tools.