Resets the absolute flux bounds of reactions proportional to the flux through the biomass reaction.
Usage
fluxBMCoupling(
model,
BMreact = guessBMReaction(model),
cpl_c = 400,
cpl_u = 0.01
)Arguments
- model
Community model of class ModelComm
- BMreact
IDs of individual biomass reactions
- cpl_c
Coupling constraint
c- cpl_u
Coupling constraint
u
Details
The idea of flux coupling in flux balance models of multi-species communities was first introduced by Heinken et al. (2013). The idea is to limit the reactions fluxes in order to prevent that a reaction in one organism is solely used (i.e., carries a non-zero flux) to benefit another organism in the community and not the organism that produced the enzyme for the specific reaction. Therefore, new linear constraints are added to the flux balance model where the absolute reaction flux bounds of organism j is proportional to the biomass formation of organism j. The coupling constraints are defined as:
$$-c v_{b,j} - u \leq v_{i,j} \leq c v_{b,j} + u$$
where \(v_{i,j}\) is the flux through reaction i in organism j, \(v_{b,j}\) the biomass reaction of organism j. c and u are parameters for the coupling constraints that define intercept (u) and slope (c) (see figure).
References
Heinken A, Sahoo S, Fleming RMT, Thiele I. Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Vol. 4, Gut Microbes; 2013. http://dx.doi.org/10.4161/gmic.22370