ROOM

ROOM(model, fluxWT, rxnKO, varargin)

Performs a MILP version of the ROOM (Regulatory on/off minimization of metabolic flux changes) approach

USAGE:

[fluxROOM, solutionROOM, totalFluxDiff] = ROOM(model, WTflux, rxnKO, delta, epsilon, printLevel)

INPUTS:

model: Metabolic model fluxWT: Numeric array with flux distribution of wild type rxnKO: List of perturbations performed to the model

(reactions that are eliminated)

OPTIONAL INPUTS:

delta: Multiplicative tol for flux change (Default = 0.03) epsilon: Additive tolerance for flux change (Default = 0.001) printLevel: Verbose output (Default = 1)

OUTPUTS:

fluxROOM: Flux distribution after ROOM calculation solutionROOM: Solution structure totalFluxDiff: Euclidean distance of ROOM objective, i.e.

\(\sum (v_{wt}-v_{del})^2\)

Solve the following problem:

\[\begin{split}min ~&~ \sum y_{i} \\ ~&~ S_{del}v_{del} = 0 \\ ~&~ lb_{del} \leq v_{del} \leq ub_{del} \\ ~&~ for i=1:nRxns\\ ~&~ v_{i} - y_{i}(v_{max,i}-w_{wt,i}^u) \leq w_{wt,i}^u \\ ~&~ v_{i} - y_{i}(v_{min,i}-w_{wt,i}^l) \geq w_{wt,i}^l \\ ~&~ y_{i} \in {0,1} \\ ~&~ w_{wt,i}^u = w_{wt,i} + \delta |w_{wt,i}| + \epsilon \\ ~&~ w_{wt,i}^l = w_{wt,i} - \delta |w_{wt,i}| - \epsilon \\\end{split}\]

NOTE:

The code here has been based on:
Shlomi, T., Berkman, O., & Ruppin, E. (2005). Regulatory on/off
minimization of metabolic flux changes after genetic perturbations.
Proceedings of the National Academy of Sciences, 102(21), 7695-7700

linearROOM(model, fluxWT, rxnKO, varargin)

Performs a LP version of the ROOM (Regulatory on/off minimization of metabolic flux changes) approach

USAGE:

[fluxROOM, solutionROOM, totalFluxDiff] = linearROOM(model, WTflux, rxnKO, delta, epsilon, printLevel)

INPUTS:

model: Metabolic model fluxWT: Numeric array with flux distribution of wild type rxnKO: List of perturbations performed to the model

(reactions that are eliminated)

OPTIONAL INPUTS:

delta: Multiplicative tol for flux change (Default = 0.03) epsilon: Additive tolerance for flux change (Default = 0.001) printLevel: Verbose output (Default = 1)

OUTPUTS:

fluxROOM: Flux distribution after ROOM calculation solutionROOM: Solution structure totalFluxDiff: Euclidean distance of ROOM objective, i.e.

\(\sum (v_{wt}-v_{del})^2\)

Solve the following problem:

\[\begin{split}min ~&~ \sum y_{i} \\ ~&~ S_{del}v_{del} = 0 \\ ~&~ lb_{del} \leq v_{del} \leq ub_{del} \\ ~&~ for i=1:nRxns\\ ~&~ v_{i} - y_{i}(v_{max,i}-w_{wt,i}^u) \leq w_{wt,i}^u \\ ~&~ v_{i} - y_{i}(v_{min,i}-w_{wt,i}^l) \geq w_{wt,i}^l \\ ~&~ 0 \leq y_{i} \leq 1 \\ ~&~ w_{wt,i}^u = w_{wt,i} + \delta |w_{wt,i}| + \epsilon \\ ~&~ w_{wt,i}^l = w_{wt,i} - \delta |w_{wt,i}| - \epsilon \\\end{split}\]

NOTE:

The code here has been based on:
Shlomi, T., Berkman, O., & Ruppin, E. (2005). Regulatory on/off
minimization of metabolic flux changes after genetic perturbations.
Proceedings of the National Academy of Sciences, 102(21), 7695-7700