Mechanistic models can help to better understand the behavior of a
biological system in response to drugs. We present logic modeling as
an approach to understand deregulation of signal transduction in
disease and to characterize a drug's mode of action. We discuss a
workflow for building a logic model from literature and experimental
data and analyze the resulting model to obtain insights of relevance
for systems pharmacology. Among the tools that can be used, we discuss
OmniPath (network reconstruction from the literature), CellNOpt (model
fit to experimental data), MaBoSS (model analysis), PHONEMeS (data
driven reconstruction), and Cytoscape (visualization). We showcase the
application of this workflow to the study of prostate cancer.