Quantitative Molecular Models for Biological Processes: Modeling of Signal Transduction Networks with ANIMO

Computational modeling of biological networks is increasing in popularity due to the increased demand for understanding biological processes. This understanding requires integration of a variety of experimental data that allows understanding of complex mechanisms regulating cell and tissue function. However, the mathematical complexity of many modeling tools have thusfar prevented broad adaptation and effective use by molecular biologists. In this chapter, we show by example how one can start building a model in ANIMO and how to adapt the model to experimental data. We show how this model can be used for simulating network activities, testing hypotheses, and how to improve the model using wet-lab data.