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Merge pull request #1477 from opencobra/develop
Regular merge of develop
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‎deprecated/OMNI.m

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function [OMNISol,bilevelMILPProblem] = OMNI(model, selectedRxnList, options, constrOpt, measOpt, prevSolutions, verbFlag)
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%
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%% ***********************NOT WORKING**************************************
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%
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%function [OMNISol,bilevelMILPProblem] = OMNI(model,selectedRxnList,options,constrOpt,prevSolutions,verbFlag,solutionFileNameTmp)
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%OMNI Run OMNI in the most general form
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%
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% OMNI(model,selectedRxnList,options,constrOpt,prevSolutions,verbFlag,solutionFileName)
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%
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%INPUTS
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% model Structure containing all necessary variables to
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% describe a stoichiometric model
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% rxns Rxns in the model
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% mets Metabolites in the model
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% S Stoichiometric matrix (sparse)
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% b RHS of Sv = b (usually zeros)
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% c Objective coefficients
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% lb Lower bounds for fluxes
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% ub Upper bounds for fluxes
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% rev Reversibility of fluxes
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% selectedRxnList List of reactions that can be knocked-out in OMNI
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% options OMNI options
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% numDel # of bottlenecks
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% numDelSense Direction of # of bottleneck constraint (G/E/L)
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% vMax Max flux
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% solveOMNI Solve problem within Matlab
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% createGams Create GAMS input file
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% gamsFile GAMS input file name
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% constrOpt Explicitly constrained reaction options
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% rxnList Reaction list
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% values Values for constrained reactions
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% sense Constraint senses for constrained reactions
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% (G/E/L)
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% measOpt Measured flux options
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% rxnSel Names of measured reactions
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% values Flux values of measured reactions
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% weights Weights for measured fluxes
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%
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%OPTIONAL INPUTS
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% prevSolutions Previous solutions
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% verbFlag Verbose flag
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% solutionFileName File name for storing temporary solutions
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%
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%OUTPUTS
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% OMNISol OMNI solution structure
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% bilevelMILPProblem bi-level MILP problem structure used
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%
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% Markus Herrgard 3/28/05
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% Set these for MILP callbacks
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global MILPproblemType;
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global selectedRxnIndIrrev;
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%global rxnList;
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global irrev2rev;
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%global solutionFileName;
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%global biomassRxnID;
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%global OMNIKOrxnList;
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%global OMNIObjective;
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%global OMNIGrowth;
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%global solID;
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if (nargin < 5)
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prevSolutions = [];
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end
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if (nargin < 6)
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verbFlag = false;
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end
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% if (nargin < 7)
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% solutionFileName = 'OMNISolutions.mat';
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% else
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% solutionFileName = solutionFileNameTmp;
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% end
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% Convert to irreversible rxns
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[modelIrrev,matchRev,rev2irrev,irrev2rev] = convertToIrreversible(model);
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% Create the index of the previous KO's suggested by OMNI to avoid obtaining the same
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% solution again
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selPrevSolIrrev = [];
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for i = 1:size(prevSolutions,2)
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prevSolRxnList = model.rxns(prevSolutions(:,i)==1);
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selPrevSol = ismember(model.rxns,prevSolRxnList);
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selPrevSolIrrev(:,i) = selPrevSol(irrev2rev);
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end
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[nMets,nRxns] = size(modelIrrev.S);
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% Create matchings for reversible reactions in the set selected for KOs
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% This is to ensure that both directions of the reaction are knocked out
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selSelectedRxn = ismember(model.rxns,selectedRxnList);
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selSelectedRxnIrrev = selSelectedRxn(irrev2rev);
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selectedRxnIndIrrev = find(selSelectedRxnIrrev);
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cnt = 0;
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%prevRxnID = -10;
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nSelected = length(selectedRxnIndIrrev);
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selRxnCnt = 1;
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while selRxnCnt <= nSelected
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rxnID = selectedRxnIndIrrev(selRxnCnt);
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if (matchRev(rxnID)>0)
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cnt = cnt + 1;
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selectedRxnMatch(cnt,1) = selRxnCnt;
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selectedRxnMatch(cnt,2) = selRxnCnt+1;
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selRxnCnt = selRxnCnt + 1;
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end
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selRxnCnt = selRxnCnt + 1;
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end
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% Set inner constraints for the LP
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constrOptIrrev = setConstraintsIrrevModel(constrOpt,model,modelIrrev,rev2irrev);
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% constrOptIrrev = model;
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% constrOptIrrev = [];
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% Set objectives for linear and integer parts
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cLinear = zeros(nRxns,1);
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cInteger = zeros(sum(selSelectedRxnIrrev),1);
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% Set the correct objective coefficient (not necessary for OMNI)
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% targetRxnID = find(ismember(model.rxns,options.targetRxn));
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% targetRxnIDirrev = rev2irrev{targetRxnID}(1);
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% cLinear(targetRxnIDirrev) = 1;
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% Set measured reaction in objective
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sel_meas_rxn = measOpt.rxnSel';
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b_meas_rxn = measOpt.values';
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wt_meas_rxn = measOpt.weights';
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n_m = length(sel_meas_rxn);
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% Create selection vector in the decoupled representation
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% This is to ensure that the objective function for measured reversible
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% reactions is constructed correctly
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sel_m = zeros(nRxns,1);
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ord_ir = [];
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b_meas_tmp = [];
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wt_meas_tmp = [];
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for i = 1:n_m
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rxn_name = sel_meas_rxn{i};
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rxn_id = find(strcmp(model.rxns,rxn_name));
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if (~isempty(rxn_id)) % Protect against measured fluxes that are not part of the model
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b_meas_tmp = [b_meas_tmp;b_meas_rxn(i)];
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wt_meas_tmp = [wt_meas_tmp;wt_meas_rxn(i)];
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% Reversible rxns
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if (model.rev(rxn_id))
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rxn_id_ir = rev2irrev{rxn_id}(1);
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sel_m(rxn_id_ir) = 1;
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sel_m(rxn_id_ir+1) = -1;
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else
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% Irrev rxns
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rxn_id_ir = rev2irrev{rxn_id};
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sel_m(rxn_id_ir) = 1;
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end
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% Figure out ordering in decoupled representation
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ord_ir = [ord_ir rxn_id_ir];
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end
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end
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% Get ordering indices
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[tmp,ord_ind] = sort(ord_ir);
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% Reorder or create weights
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if (sum(wt_meas_rxn) == 0)
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measOpts.weights = ones(n_m,1);
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else
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measOpts.weights = wt_meas_tmp(ord_ind);
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end
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% Reorder measured flux values
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measOpts.values = b_meas_tmp(ord_ind);
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measOpts.rxnSel = sel_m;
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% Create the constraint matrices for the bilevel MILP
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bilevelMILPProblem = createBilevelMILPproblem(modelIrrev,cLinear,cInteger,selSelectedRxnIrrev,...
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selectedRxnMatch,constrOptIrrev,measOpts,options,selPrevSolIrrev);
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% Initial guess (random)
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%bilevelMILPProblem.x0 = round(rand(length(bilevelMILPProblem.c),1));
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if isfield(options,'initSolution')
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if (length(options.initSolution) > options.numDel | ~all(ismember(options.initSolution,selectedRxnList)))
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warning('Initial solution not valid - starting from a random initial solution')
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bilevelMILPProblem.x0 = [];
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else
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% Set initial integer solution
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selInitRxn = ismember(model.rxns,options.initSolution);
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selInitRxnIrrev = selInitRxn(irrev2rev);
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initRxnIndIrrev = find(selInitRxnIrrev);
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initIntegerSol = ~ismember(selectedRxnIndIrrev,initRxnIndIrrev);
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selInteger = bilevelMILPProblem.vartype == 'B';
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[nConstr,nVar] = size(bilevelMILPProblem.A);
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bilevelMILPProblem.x0 = nan(nVar,1);
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bilevelMILPProblem.x0(selInteger) = initIntegerSol;
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% LPproblem.b = bilevelMILPProblem.b - bilevelMILPProblem.A(:,selInteger)*initIntegerSol;
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% LPproblem.A = bilevelMILPProblem.A(:,bilevelMILPProblem.vartype == 'C');
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% LPproblem.c = bilevelMILPProblem.c(bilevelMILPProblem.vartype == 'C');
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% LPproblem.lb = bilevelMILPProblem.lb(bilevelMILPProblem.vartype == 'C');
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% LPproblem.ub = bilevelMILPProblem.ub(bilevelMILPProblem.vartype == 'C');
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% LPproblem.osense = -1;
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% LPproblem.csense = bilevelMILPProblem.csense;
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% LPsol = solveCobraLP(LPproblem);
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%
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% bilevelMILPProblem.x0(~selInteger) = LPsol.full;
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end
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else
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bilevelMILPProblem.x0 = [];
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end
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% Minimize
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bilevelMILPProblem.osense = 1;
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if (verbFlag)
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[nConstr,nVar] = size(bilevelMILPProblem.A);
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nInt = length(bilevelMILPProblem.intSolInd);
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fprintf('MILP problem with %d constraints %d integer variables and %d continuous variables\n',...
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nConstr,nInt,nVar);
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end
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bilevelMILPProblem.model = modelIrrev;
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% Set these for CPLEX callbacks
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MILPproblemType = 'OMNI';
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% rxnList = model.rxns;
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% biomassRxnID = find(modelIrrev.c==1);
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% solID = 0;
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% OMNIObjective = [];
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% OMNIGrowth = [];
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% OMNIKOrxnList = {};
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% Solve problem
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if (options.solveOMNI)
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OMNISol = solveCobraMILP(bilevelMILPProblem,'printLevel',0);
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if OMNISol.stat~=0
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if (~isempty(OMNISol.cont))
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OMNISol.fluxes = convertIrrevFluxDistribution(OMNISol.cont(1:length(matchRev)),matchRev);
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end
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if (~isempty(OMNISol.int))
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% Figure out the KO reactions
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OMNIRxnInd = selectedRxnIndIrrev(OMNISol.int < 1e-4);
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OMNISol.kos = model.rxns(unique(irrev2rev(OMNIRxnInd)));
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% %sanity check
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% modelTemp = changeRxnBounds(model,OMNISol.kos,0,'b');
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% solTemp = optimizeCbModel(modelTemp);
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% if abs(solTemp.f - OMNISol.obj) > 1e-4
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% [OMNISol,bilevelMILPProblem] = OMNI(model, selectedRxnList, options, constrOpt, measOpt, prevSolutions, verbFlag);
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% previous_solutions(:,end+1) = zeros(length(model.rxns),1);
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% end
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end
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else
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OMNISol.fluxes=[];
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OMNISol.kos={};
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end
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else
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OMNISol.rxnList = {};
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OMNISol.fluxes = [];
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end
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‎deprecated/_cardOpt_tangiCode/Recon2_RelaxFBA_driver_old.m

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changeCobraSolver('gurobi6','all');
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%Load data
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% Load the stoichiometrically consistent par of Recon2
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load 'Recon2.v04_sc.mat';
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[m,n] = size(model.S);
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model_Ex = findSExRxnInd(model);
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intRxnBool = model_Ex.SIntRxnBool;
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exRxnBool = true(size(intRxnBool));
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exRxnBool(find(intRxnBool)) = false;
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%Relax the model to make it flux conssitent
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relaxOption.internalRelax = 2;
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relaxOption.exchangeRelax = 2;
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relaxOption.steadyStateRelax = 1;
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relaxOption.nbMaxIteration = 1000;
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relaxOption.epsilon = 10e-6;
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relaxOption.gamma0 = 100; %trade-off parameter of l0 part of v
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relaxOption.gamma1 = 10; %trade-off parameter of l1 part of v
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relaxOption.lambda0 = 10; %trade-off parameter of l0 part of r
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relaxOption.lambda1 = 0; %trade-off parameter of l1 part of r
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relaxOption.alpha0 = 10; %trade-off parameter of l0 part of p and q
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relaxOption.alpha1 = 0; %trade-off parameter of l1 part of p and q
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relaxOption.theta = 2; %parameter of capped l1 approximation
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solution = relaxFBA(model,relaxOption);
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[v,r,p,q] = deal(solution.v,solution.r,solution.p,solution.q);
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if solution.stat == 1
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maxUB = max(model.ub);
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minLB = min(model.lb);
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display(strcat('Number of relaxations on internal reactions:',num2str(size(find(p>0 & intRxnBool),1)+size(find(q>0 & intRxnBool),1))));
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intRxnFiniteBound = ((model.ub < maxUB) & (model.lb > minLB)) & intRxnBool;
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display(strcat(' - Relaxations on internal reactions with finite bounds:',num2str(size(find(p>0 & intRxnFiniteBound),1)+size(find(q>0 & intRxnFiniteBound),1))));
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display(strcat('Number of relaxations on exchange reactions:',num2str(size(find(p>0 & exRxnBool),1)+size(find(q>0 & exRxnBool),1))));
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exRxn00 = ((model.ub == 0) & (model.lb == 0)) & exRxnBool;
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display(strcat(' - Relaxations on exchange reactions of type [0,0]:',num2str(size(find(p>0 & exRxn00),1)+size(find(q>0 & exRxn00),1))));
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display(strcat('Number of relaxations on steady state constraints:',num2str(size(find(abs(r)>0),1))));
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display(strcat('Reactions unblocked = ',num2str(length(find(abs(v)>1e-4 & ~model.rbool)))));
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else
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disp('Can not find any solution');
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end

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