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Fig. 1 | BMC Systems Biology

Fig. 1

From: DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

Fig. 1

An overview of the computational framework. The pipeline consists of seven stages. The first of these (Steps 1-2) parses a genome-scale SBML model such that the reactions and components within the system are listed. At the same time, the list of databases to be searched is registered and the kinetic rates for each reaction in the metabolic network are found (Steps 3-4). Upon obtaining the kinetic rates, PB is used to obtain thermodynamically feasible parameter distributions (Step 5). Using these parameter values, the SBML model is then translated into a set of ordinary differential equations representing the dynamic changes in system components (Step 6). Finally, the parameterised model can be simulated and analysed (Step 7)

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