An application example of how to use FBA-SimVis is provided for a small metabolic network.
This network happens to be a subnet for flavonoid metabolism in Arabidopsis thaliana extracted from the Aracyc [ 19] database, but serves here merely as a realistic example of a small metabolic network.
Comment: A possible nice way to improve the manuscript, which might increase its potential impact a little bit, would be to extend the analysis to consider a (small) metabolic network, meaning a system with more than one reaction.
The resulting algorithm was effective given small metabolic networks of primary metabolism and the use of nonlinear programming methods.
Although successful in these relatively small metabolic networks, a criticism expressed by several authors [ 11, 12, 15] is that it relies totally on a local property, the degree of node connectivity, and takes no account of the global network structure.
The MCS algorithm of Klamt and Gilles is not applicable to the genome-scale due to its dependence on elementary mode computation, which is only feasible for small metabolic networks (i.e. less than 300 reactions) [ 4, 10, 11, 13].
It has been increasingly studied around the world for scientific purposes, especially for its genome, biology, physiology, and also for the analysis of its small-scale metabolic network.
Overall, our framework could potentially be more useful to steer rapid development of a broad range of organisms on the basis of a representative small-scale metabolic network.
Conserved enzyme subnetworks in pyrimidine and alanine, aspartate, glutamate networks In this experiment, we used smaller metabolic network data sets (i.e., Eukaryote-AAG, Prokaryote-AAG, Eukaryote-P and Prokaryote-P).
These quasi-steady state methods have been used for the simulation of model microorganisms, where relatively small-scale metabolic networks have been integrated with dynamic models of regulatory processes.
Most of this decrease is caused by the fact that smaller metabolic networks are less likely to contain all super-essential reactions, reactions that any network must contain to be viable in a given environment.
