Merge pull request #210 from opencobra/develop

Develop

analysis/benchmarkSolvers/driver_loadBenchmarkWBMsolvers.m

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+%% Choose between different models. 
+% Add your own via the switch statement below.
+
+if ~exist(modelToUse,'var')
+    %modelToUse  = 'iCoreED'; % medium - TODO could not compute extremePools -find out why.
+    %modelToUse = 'iDopaNeuroC';
+    % modelToUse = 'Recon3T';
+    modelToUse = 'Harvey';
+    %modelToUse = 'Harvetta';
+end
+
+%% Set local parameters
+% If true, it will relax tight bounds
+relaxTightBounds=0;
+lowerExponent = 4; %the minimum difference between ub_j and lb_j is 10^(lowerExponent)
+higherExponent = 10;
+
+% Load the selected model and make any adjustments necessary.
+switch modelToUse
+    case 'iCoreED'
+        if ~exist('iCoreED','var')
+            load ~/drive/sbgCloud/projects/variationalKinetics/data/iCoreED/iCoreED_modelT.mat
+        end
+        model    = modelT;
+
+        if ~isfield(model,'biomassRxnAbbr')
+            model.biomassRxnAbbr='Biomass_Ecoli_core_w_GAM';
+        end
+    case 'iDopaNeuroC'
+        load('~/drive/sbgCloud/projects/variationalKinetics/data/iDopaNeuro/iDopaNeuroC.mat')
+        %load('~/drive/sbgCloud/data/models/published/iDopaNeuro/iDopaNeuroC.mat')
+        model = iDopaNeuroC;
+        model.description='iDopaNeuroC';
+        model.version='1.0';
+    case 'Recon3T'
+        load('~/drive/sbgCloud/projects/variationalKinetics/data/Recon3T/Recon3DModel_301_xomics_input.mat');
+    case 'Harvey'
+        if isfile('~/drive/sbgCloud/code/wbm_modelingcode/WBM_reconstructions/Harvey_1_04c_lifted.mat')
+            load('~/drive/sbgCloud/code/wbm_modelingcode/WBM_reconstructions/Harvey_1_04c_lifted.mat')
+            model=male;
+            model.osenseStr='max';
+        else
+            load('~/drive/sbgCloud/code/wbm_modelingcode/WBM_reconstructions/Harvey_1_04c.mat')
+            %load('~/drive/sbgCloud/projects/variationalKinetics/data/WBM/Harvey_1_04c.mat')
+            %load('~/drive/sbgCloud/data/models/published/Harvey_Harvetta/20191104_Harvey_1_01c.mat')
+            model=male;
+            model.osenseStr='max';
+            model = changeObjective(model,model.rxns(contains(model.rxns,'Whole')));
+
+            model = homogeniseCouplingConstraints(model);
+
+            %% Reformulate coupling constraints
+            % Using hierarchical lifting as described here
+            % https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-240
+            [male] = liftCouplingConstraints(model);
+            save('~/drive/sbgCloud/code/wbm_modelingcode/WBM_reconstructions/Harvey_1_04c_lifted.mat','male');
+            return
+        end
+
+    case 'Harvetta'
+        if isfile('~/drive/sbgCloud/code/wbm_modelingcode/WBM_reconstructions/Harvetta_1_04c_lifted.mat')
+            load('~/drive/sbgCloud/code/wbm_modelingcode/WBM_reconstructions/Harvetta_1_04c_lifted.mat')
+            model=female;
+            model.osenseStr='max';
+        else
+            load('~/drive/sbgCloud/code/wbm_modelingcode/WBM_reconstructions/Harvetta_1_04c.mat')
+            %load('~/drive/sbgCloud/projects/variationalKinetics/data/WBM/Harvetta_1_04c.mat')
+            %load('~/drive/sbgCloud/data/models/published/Harvey_Harvetta/20191104_Harvetta_1_01c.mat')
+            model=female;
+            model.osenseStr='max';
+            model = changeObjective(model,model.rxns(contains(model.rxns,'Whole')));
+
+            model = homogeniseCouplingConstraints(model);
+
+            %% Reformulate coupling constraints
+            % Using hierarchical lifting as described here
+            % https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-240
+            [female] = liftCouplingConstraints(model);
+            save('~/drive/sbgCloud/code/wbm_modelingcode/WBM_reconstructions/Harvetta_1_04c_lifted.mat','female');
+            return
+        end
+    otherwise
+        errror('Unrecognised modelToUse')
+end
+
+
+