"sysBiolAlg_mtf"sysBiolAlg_mtf holds an object of class
optObj which is generated to meet the
requirements of the minimize total flux algorithm: minimize the absolute sum
of all fluxes given a previously calculated objective value.sysBiolAlg(model, algorithm = "mtf", ...).
Arguments to ... which are passed to method initialize of class
sysBiolAlg_mtf are described in the Details section."sysBiolAlg ", directly.initialize method has the following arguments:
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object] The problem object is built to be capable to perform minimize total flux
with a given model, which is basically the solution of a linear programming
problem
$$\begin{array}{rll} \min & \begin{minipage}[b]{2.5em}
\[
\sum_{i=1}^n cost_i |v_i|
\]
\end{minipage} \[2em]
\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]
& \mbox{\boldmath$c$\unboldmath}_{\mathrm{wt}} \geq
\mbox{\boldmath$c$\unboldmath}^{\mathrm{T}}
\mbox{\boldmath$v$\unboldmath}_{\mathrm{wt}} \[1ex]
\end{array}$$
with
$\mbox{\boldmath$c$\unboldmath}^{\mathrm{T}}
\mbox{\boldmath$v$\unboldmath}_{\mathrm{wt}}$
beeing the previously computed optimized value of the objective function
(argument wtobj).
The variable $\bold{S}$ denotes the stoichiometric matrix,
$\alpha_i$ and $\beta_i$ beeing the lower and upper bounds
for flux (variable) $i$. The total number of variables of the
optimization problem is denoted by $n$.
The optimization can be executed by using optimizeProb.
sysBiolAlg and
superclass sysBiolAlg.