ABSTRACT
This chapter demonstrates how complementary software tools can be combined in a consistent and reproducible workflow to analyze a model of CD4 T cell differentiation. Cellular signalling pathways enable a cell to detect and respond to changes in its environment. An appropriate response of a cell towards specific stimuli is the basis for processes such as development, adaptation and immune response. The chapter utilizes mathematical modelling and computational analysis to describe cell signalling and to gain a deeper understanding of the regulatory mechanisms. It focuses on the nuclear factor-κB (NF-κB) signalling pathway which is often dysregulated in tumours but also in other diseases. The chapter explores the effects of different regulatory processes, e.g. feedback regulation, post-transcriptional modifications or cross-talk on the dynamical properties of the pathway and shows how quantitative modelling can be employed to identify new regulatory layers. The development of cancer is associated with an accumulation of perturbations in cells, such as mutations or abnormal expression of proteins.
