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Recent proposals for such system designs have looked at small and/or medium scale networks employing hybrid interconnects.
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A medium scale network has typically a very large number of EMs in the order of ~106 [ 21].
This medium scale network has a total of 251 EMs, which represent, in the context of the present study, the universe of cellular functions to be screened against envirome components.
Due to the convexity properties of the model, global optimal solutions are achieved through the standard branch-and-bound procedure with commercial optimisation solvers, but use of this optimisation framework is limited to small-medium scale networks due to NP-hardness.
Although existing algorithms have been demonstrated to work well on medium-scale networks, they have two inherent drawbacks.
Biologically, computationally, and mathematically, parameter estimation remains a significant challenge for the modeling of gene regulatory dynamics, even for medium-scale networks of just 5 10 interacting genes, (Cao and Zhao 2008; Lillacci and Khammash 2010; Kuwahara et al. 2013; Fan et al. 2015).
Additional file 16 Irreversibility matrix for the medium-scale network.
(62×68) S int matrix for the medium-scale network, in Microsoft Office Excel format.
Additional file 15 Combined extracellular and biomass stoichiometric matrix for the medium-scale network.
Lists of reactions, intracellular and extracellular metabolites for the medium-scale network, in Microsoft Office Word format.
Additional file 14 Intracellular stoichiometric matrix for the medium-scale network.
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