We present in this article a methodology for designing kinetic models of molecular signaling networks, which was exemplarily applied for modeling one of the Ras/MAPK signaling pathways in the mouse Y1 adrenocortical cell line. The methodology is interdisciplinary, that is, it was developed in a way that both dry and wet lab teams worked together along the whole modeling process.
Keywords: Cell signaling pathways; Differential-algebraic equation; ELISA; ERK; MAPK; Model simplification; Model-fitting analysis; Nonlinear optimization; Ordinary differential equation; Ras; Western blot.