"sysBiolAlg_fba"sysBiolAlg_fba holds an object of class
optObj which is generated to meet the
requirements of the FBA algorithm.sysBiolAlg(model, algorithm = "fba", ...).
Arguments to ... which are passed to method initialize of class
sysBiolAlg_fba are described in the Details section."sysBiolAlg ", directly.initialize method has the following arguments:
[object Object],[object Object],[object Object],[object Object] The problem object is built to be capable to perform flux balance analysis
(FBA) with a given model, which is basically the solution of a linear
programming problem
$$\begin{array}{rll} \max & \mbox{\boldmath$c$\unboldmath}^{\mathrm{T}}
\mbox{\boldmath$v$\unboldmath} \[1ex]
\mathrm{s.\,t.} & \mbox{\boldmath$Sv$\unboldmath} = 0 \[1ex]
& \alpha_i \leq v_i \leq \beta_i
& \quad \forall i \in {1, \ldots, n} \[1ex]
\end{array}$$
with $\bold{S}$ beeing the stoichiometric matrix, $\alpha_i$
and $\beta_i$ beeing the lower and upper bounds for flux (variable)
$i$ respectively. The total number of variables of the optimization
problem is denoted by $n$. The solution of the optimization is a flux
distribution maximizing the objective function
$\mbox{\boldmath$c$\unboldmath}^{\mathrm{T}}
\mbox{\boldmath$v$\unboldmath}$ under the a given environment and the assumption of steady state.
The optimization can be executed by using optimizeProb.
sysBiolAlg and
superclass sysBiolAlg.