Schematic of the molecular logic of the G1/S (A) and G2/M (B) checkpoint models used in this study.

The G1/S model of Qu et al., is composed of 16 dynamic protein balances, 2 species constraints and 44 parameters [31]. TheG2-DNA damage model of Aguda is composed of 15 dynamic protein balances 1constraint and 40 parameters (30). Both the G1/S and G2/M models employ mass action kinetics and the parameters are linear in the mass balances. Nomenclature G1/S: CDC25A - Dual Specificity Phosphatase CDC25A, Cdk2 - Cyclin Dependent Kinase 2, Cdk4/6 - Cyclin Dependent Kinase 4 or 6, CycE - Cyclin E, CycD - Cyclin D, E2F - Transcription Factor E2F, pRB - Retinoblastoma protein, p27 - A Cyclin Dependent Kinase Inhibitor (CKI), also called Kip1. Nomenclature G2/M: pMPF - pre-Maturation Promoting Factor, a complex of CycB (Cyclin B) and Cdk1 (Cyclin Dependent Kinase1) in inactive form, MPF – active form of MPF, aCDC25 - active CDC25 phosphatase, iCDC25 – inactive form of CDC25, aCDC25(P-216) – active CDC25, phosphorylated at Serine 216 residue, iCDC25(P-216) - inactive CDC25, phosphorylated at Serine 216, 14-3-3σ - 14-3-3σ protein. In both the schematics, small red circles with P represent phosphate group, a (+) sign implies positive regulation whereas a (−) sign represents negative regulation.