Lloyd Catherine May c.lloyd@auckland.ac.nz The University of Auckland The Bioengineering Institute 2003-01-27 The University of Auckland, Bioengineering Institute A Generic Model Of Glycolysis with encapsulation of the side chain reactions Below is a CellML description of a general model of the metabolic pathway glycolysis with encapsulation of the side chain reactions. The purpose of this description is to illustrate how CellML can be used to model a general metabolic pathway. Catherine Lloyd Homo sapiens Bronk J Ramsey Human Metabolism 1999 Addison Wesley Longman Limited location England $\frac{d \mathrm{Glycogen}}{d \mathrm{time}}=\mathrm{delta\_Glycogen\_rxn2}+\mathrm{delta\_Glycogen\_rxn0}$ $\frac{d \mathrm{UDP}}{d \mathrm{time}}=\mathrm{delta\_UDP\_rxn2}$ $\frac{d \mathrm{UDP\_glucose}}{d \mathrm{time}}=\mathrm{delta\_UDP\_glucose\_rxn3}+\mathrm{delta\_UDP\_glucose\_rxn2}$ $\frac{d \mathrm{Pi}}{d \mathrm{time}}=\mathrm{delta\_Pi\_rxn1}+\mathrm{delta\_Pi\_rxn6}+\mathrm{delta\_Pi\_rxn9}+\mathrm{delta\_Pi\_rxn11}+\mathrm{delta\_Pi\_rxn0}$ $\frac{d \mathrm{Glucose\_1\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Glucose\_1\_phosphate\_rxn0}+\mathrm{delta\_Glucose\_1\_phosphate\_rxn3}+\mathrm{delta\_Glucose\_1\_phosphate\_rxn4}+\mathrm{delta\_Glucose\_1\_phosphate\_rxn5}+\mathrm{delta\_Glucose\_1\_phosphate\_rxn6}$ $\frac{d \mathrm{UTP}}{d \mathrm{time}}=\mathrm{delta\_UTP\_rxn3}$ $\frac{d \mathrm{PPi}}{d \mathrm{time}}=\mathrm{delta\_PPi\_rxn3}+\mathrm{delta\_PPi\_rxn1}$ $\frac{d \mathrm{Glucose}}{d \mathrm{time}}=\mathrm{delta\_Glucose\_rxn6}+\mathrm{delta\_Glucose\_rxn5}$ $\frac{d \mathrm{ATP}}{d \mathrm{time}}=\mathrm{delta\_ATP\_rxn20}+\mathrm{delta\_ATP\_rxn5}+\mathrm{delta\_ATP\_rxn8}+\mathrm{delta\_ATP\_rxn10}+\mathrm{delta\_ATP\_rxn15}$ $\frac{d \mathrm{ADP}}{d \mathrm{time}}=\mathrm{delta\_ADP\_rxn5}+\mathrm{delta\_ADP\_rxn8}+\mathrm{delta\_ADP\_rxn10}+\mathrm{delta\_ADP\_rxn15}+\mathrm{delta\_ADP\_rxn20}$ $\frac{d \mathrm{H2O}}{d \mathrm{time}}=\mathrm{delta\_H2O\_rxn19}+\mathrm{delta\_H2O\_rxn6}+\mathrm{delta\_H2O\_rxn9}+\mathrm{delta\_H2O\_rxn11}$ $\frac{d \mathrm{Glucose\_6\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Glucose\_6\_phosphate\_rxn4}+\mathrm{delta\_Glucose\_6\_phosphate\_rxn7}$ $\frac{d \mathrm{Fructose\_6\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Fructose\_6\_phosphate\_rxn9}+\mathrm{delta\_Fructose\_6\_phosphate\_rxn11}+\mathrm{delta\_Fructose\_6\_phosphate\_rxn7}+\mathrm{delta\_Fructose\_6\_phosphate\_rxn8}+\mathrm{delta\_Fructose\_6\_phosphate\_rxn10}$ $\frac{d \mathrm{Fructose\_2\_6\_bisphosphate}}{d \mathrm{time}}=\mathrm{delta\_Fructose\_2\_6\_bisphosphate\_rxn8}+\mathrm{delta\_Fructose\_2\_6\_bisphosphate\_rxn9}$ $\frac{d \mathrm{Fructose\_1\_6\_bisphosphate}}{d \mathrm{time}}=\mathrm{delta\_Fructose\_1\_6\_bisphosphate\_rxn10}+\mathrm{delta\_Fructose\_1\_6\_bisphosphate\_rxn11}+\mathrm{delta\_Fructose\_1\_6\_bisphosphate\_rxn12}+\mathrm{delta\_Fructose\_1\_6\_bisphosphate\_rxn13}$ $\frac{d \mathrm{Glyceraldehyde\_3\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Glyceraldehyde\_3\_phosphate\_rxn12}+\mathrm{delta\_Glyceraldehyde\_3\_phosphate\_rxn14}+\mathrm{delta\_Glyceraldehyde\_3\_phosphate\_rxn17}$ $\frac{d \mathrm{Dihydroxyacetone\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Dihydroxyacetone\_phosphate\_rxn13}+\mathrm{delta\_Dihydroxyacetone\_phosphate\_rxn14}+\mathrm{delta\_Dihydroxyacetone\_phosphate\_rxn16}$ $\frac{d \mathrm{Glycerol}}{d \mathrm{time}}=\mathrm{delta\_Glycerol\_rxn15}$ $\frac{d \mathrm{Glycerol\_3\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Glycerol\_3\_phosphate\_rxn15}+\mathrm{delta\_Glycerol\_3\_phosphate\_rxn16}$ $\frac{d \mathrm{NAD}}{d \mathrm{time}}=\mathrm{delta\_NAD\_rxn16}+\mathrm{delta\_NAD\_rxn21}+\mathrm{delta\_NAD\_rxn17}$ $\frac{d \mathrm{NADH}}{d \mathrm{time}}=\mathrm{delta\_NADH\_rxn17}+\mathrm{delta\_NADH\_rxn16}+\mathrm{delta\_NADH\_rxn21}$ $\frac{d H}{d \mathrm{time}}=\mathrm{delta\_H\_rxn17}+\mathrm{delta\_H\_rxn16}+\mathrm{delta\_H\_rxn21}$ $\frac{d \mathrm{Lactate}}{d \mathrm{time}}=\mathrm{delta\_Lactate\_rxn21}$ $\frac{d \mathrm{Pyruvate}}{d \mathrm{time}}=\mathrm{delta\_Pyruvate\_rxn20}+\mathrm{delta\_Pyruvate\_rxn21}$ $\frac{d \mathrm{Phosphoenolpyruvate}}{d \mathrm{time}}=\mathrm{delta\_Phosphoenolpyruvate\_rxn19}+\mathrm{delta\_Phosphoenolpyruvate\_rxn20}$ $\frac{d \mathrm{Phosphoglycerate\_2}}{d \mathrm{time}}=\mathrm{delta\_Phosphoglycerate\_2\_rxn18}+\mathrm{delta\_Phosphoglycerate\_2\_rxn19}$ $\frac{d \mathrm{Phosphoglycerate\_3}}{d \mathrm{time}}=\mathrm{delta\_Phosphoglycerate\_3\_rxn18}$ $\frac{d \mathrm{Bisphosphoglycerate\_1\_3}}{d \mathrm{time}}=\mathrm{delta\_Bisphosphoglycerate\_1\_3\_rxn17}$ $\mathrm{rate}=\frac{\mathrm{vmax0}\mathrm{Glycogen}\mathrm{Pi}}{\mathrm{km0}+\mathrm{Glycogen}+\mathrm{Pi}}$ $\mathrm{rate}=\frac{\mathrm{PPi}\mathrm{vmax1}}{\mathrm{km1}+\mathrm{PPi}}$ $\mathrm{rate}=\frac{\mathrm{UDP\_glucose}\mathrm{vmax2}}{\mathrm{km2}+\mathrm{UDP\_glucose}}$ $\mathrm{rate}=\frac{\mathrm{UTP}\mathrm{Glucose\_1\_phosphate}\mathrm{vmax3}}{\mathrm{km3}+\mathrm{UTP}+\mathrm{Glucose\_1\_phosphate}}$ $\mathrm{rate}=\frac{\mathrm{ATP}\mathrm{Glucose}\mathrm{vmax5}}{\mathrm{km5}+\mathrm{ATP}+\mathrm{Glucose}}$ $\mathrm{rate}=\frac{\mathrm{H2O}\mathrm{Glucose\_1\_phosphate}\mathrm{vmax6}}{\mathrm{km6}+\mathrm{H2O}+\mathrm{Glucose\_1\_phosphate}}$ $\mathrm{rate}=\frac{\mathrm{ATP}\mathrm{Fructose\_6\_phosphate}\mathrm{vmax8}}{\mathrm{km8}+\mathrm{ATP}+\mathrm{Fructose\_6\_phosphate}}$ $\mathrm{rate}=\frac{\mathrm{H2O}\mathrm{Fructose\_2\_6\_bisphosphate}\mathrm{vmax9}}{\mathrm{km9}+\mathrm{H2O}+\mathrm{Fructose\_2\_6\_bisphosphate}}$ $\mathrm{rate}=\frac{\mathrm{ATP}\mathrm{Fructose\_6\_phosphate}\mathrm{vmax10}}{\mathrm{km10}+\mathrm{ATP}+\mathrm{Fructose\_6\_phosphate}}$ $\mathrm{rate}=\frac{\mathrm{H2O}\mathrm{Fructose\_1\_6\_bisphosphate}\mathrm{vmax11}}{\mathrm{km11}+\mathrm{H2O}+\mathrm{Fructose\_1\_6\_bisphosphate}}$ $\mathrm{rate}=\frac{\mathrm{ATP}\mathrm{Glycerol}\mathrm{vmax15}}{\mathrm{km15}+\mathrm{ATP}+\mathrm{Glycerol}}$ $\mathrm{rate}=\frac{\mathrm{Phosphoglycerate\_2}\mathrm{vmax19}}{\mathrm{km19}+\mathrm{Phosphoglycerate\_2}}$ $\mathrm{rate}=\frac{\mathrm{Phosphoenolpyruvate}\mathrm{ADP}\mathrm{vmax20}}{\mathrm{km20}+\mathrm{Phosphoenolpyruvate}+\mathrm{ADP}}$