Strategy for three layers and two stages. A flow of the mathematical conversion according to three layers and two stages. The reactions are classified into three layers, i.e., gene, protein, and metabolic layers, and the conversion process is divided into two stages. At the first stage, both gene and protein networks are converted into the ordinary transcription and translation equations (TT), Conventional Mass Action (CMA), respectively, whereas the metabolic network uses General Mass Action (GMA) or simplified Michaelis-Menten equations (MM). At the second stage, such ordinary differential equations are further converted into differential and algebraic equations (DAEs) or S-system (Supplemental Method 1).
