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Figure 7 | BMC Systems Biology

Figure 7

From: The systems biology simulation core algorithm

Figure 7

Simulation of glycolytic oscillations. This figure displays the results of a simulation computed with the Systems Biology Simulation Core Library based on model No. 206 from BioModels Database [35, 37]. A) Shown are the changes of the concentration of the most characteristic intracellular metabolites 3-phosphoglycerate, ATP, glucose, glyceraldehyde 3-phosphate (GA3P), and NAD+ within yeast cells in the time interval [ 0, 30] seconds. B) This panel displays a selection of the dynamics of relevant fluxes (D-glucose 6-phosphotransferase, glycerone-phosphate- forming, phosphoglycerate kinase, pyruvate 2-O-phosphotransferase, acetaldehyde forming, ATP biosynthetic process) that were computed as intermediate results by the algorithm. The computation was performed using the Adams-Moulton solver [38] (KiSAO term 280) with 200 integration steps, 10−10 as absolute error tolerance and 10−5 as relative error tolerance. Due to the importance of feedback regulation the selection of an appropriate numerical solver is of crucial importance for this model. Methods without step-size adaptation, such as the fourth order Runge-Kutta algorithm (KiSAO term 64), might only be able to find a high-quality solution with an appropriate number of integration steps. The simulation results obtained by using the algorithm described in this work reproduces the results provided by BioModels Database.

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