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Figure 4 | Journal of Systems Chemistry

Figure 4

From: Evolution of metabolic networks: a computational frame-work

Figure 4

Generating Reaction Network. To avoid combinatorial explosion during reaction network generation a filtering step, which prunes unproductive parts from the reaction network, is needed after each application of the reaction set (arrows) to the (current) set of molecules (circles). The network usually quickly converges in size if the filtering is performed based on reaction kinetics. In particular, after the estimation of reaction rates (green squares), the dynamics of the reaction network is simulated by a Gillespie type stochastic method, followed by removing nodes from the reaction network which have not accumulated enough particles, due to small reaction rates.

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