Develop

documentation/source/guides/howToContribute.rst

@@ -5,7 +5,7 @@ This guide explains, step by step, how to contribute code to the COBRA Toolbox:
 how to fork the repository, work on your changes locally, place your code in the
 correct folder inside ``src``, add tests, and open a pull request (PR).
 
-1. Overview of the contribution workflow
+Overview of the contribution workflow
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The typical workflow for contributing is:
@@ -21,7 +21,7 @@ The typical workflow for contributing is:
 
 The following sections describe each step in more detail.
 
-2. Fork the COBRA Toolbox repository
+1. Fork the COBRA Toolbox repository
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 1. Go to the main COBRA Toolbox repository on GitHub:
@@ -36,7 +36,7 @@ The following sections describe each step in more detail.
 
 All your changes will be pushed to this fork.
 
-3. Clone your fork locally
+2. Clone your fork locally
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 To work on the code, clone your fork to your local machine.
@@ -56,7 +56,7 @@ To work on the code, clone your fork to your local machine.
       git remote add upstream https://github.com/opencobra/cobratoolbox.git
       git fetch upstream
 
-4. Add your code to the correct folder in ``src``
+3. Add your code to the correct folder in ``src``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 All new COBRA Toolbox code should be added under the ``src`` folder. The main
@@ -75,7 +75,7 @@ easier for others to navigate the code.
 
 Below is guidance on when to use each folder.
 
-**4.1. src/analysis**
+**3.1. src/analysis**
 
 Use ``analysis`` for methods that analyse existing metabolic models. Examples:
 
@@ -86,7 +86,7 @@ Use ``analysis`` for methods that analyse existing metabolic models. Examples:
 Suggested structure:  
 ``src/analysis/myNewAnalysisTool/``
 
-**4.2. src/base**
+**3.2. src/base**
 
 Use ``base`` for shared utilities and core methods needed across the toolbox.
 Examples include:
@@ -98,7 +98,7 @@ Examples include:
 Suggested structure:  
 ``src/base/myUtilityFunctions/``
 
-**4.3. src/dataIntegration**
+**3.3. src/dataIntegration**
 
 Use ``dataIntegration`` for code that integrates omics or experimental data with
 a model. Examples:
@@ -110,7 +110,7 @@ a model. Examples:
 Suggested structure:  
 ``src/dataIntegration/myIntegrationPipeline/``
 
-**4.4. src/design**
+**3.4. src/design**
 
 Use ``design`` for algorithms that propose modifications or interventions.
 Examples:
@@ -122,7 +122,7 @@ Examples:
 Suggested structure:  
 ``src/design/myDesignAlgorithm/``
 
-**4.5. src/reconstruction**
+**3.5. src/reconstruction**
 
 Use ``reconstruction`` for tools that construct, curate or update metabolic
 models. Examples:
@@ -134,7 +134,7 @@ models. Examples:
 Suggested structure:  
 ``src/reconstruction/myReconstructionPipeline/``
 
-**4.6. src/visualization**
+**3.6. src/visualization**
 
 Use ``visualization`` for tools that generate plots, diagrams or graphical
 summaries. Examples:
@@ -146,7 +146,7 @@ summaries. Examples:
 Suggested structure:  
 ``src/visualization/myVisualisationTools/``
 
-5. Add a test for every new code module
+4. Add a test for every new code module
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Every contribution must include a corresponding **test**. This ensures that new
@@ -162,7 +162,7 @@ For more information on writing tests, refer to:
 
 * :ref:`testGuide`
 
-6. Commit and push your changes
+5. Commit and push your changes
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Once your code and tests are ready, commit your work.
@@ -192,7 +192,7 @@ Once your code and tests are ready, commit your work.
 
       git push origin develop
 
-7. Open a pull request
+6. Open a pull request
 ~~~~~~~~~~~~~~~~~~~~~~
 
 Once your changes are pushed, open a pull request on GitHub.
@@ -218,7 +218,7 @@ Once your changes are pushed, open a pull request on GitHub.
 
 5. Submit the pull request.
 
-8. Address review comments
+7. Address review comments
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Maintainers may request revisions. This is normal.

src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/createPersonalizedModel.m

@@ -88,8 +88,7 @@
     matStart=0;
     cnt=1;
     for i = 1:length(presBac)
-        % find the indices of where there merged matrices are on the C
-        % matrix
+        % find the indices of where there merged matrices are on the C matrix
         matInd1=[];
         for j=1:size(couplingMatrixRed{i,1},1)
             matInd1(size(matInd1,1)+1,1)=j+matStart;
@@ -99,7 +98,27 @@
             pruned_model.ctrs{cnt,1}=couplingMatrixRed{i,4}{j,1};
             cnt=cnt+1;
         end
-        matInd2=find(strncmp(pruned_model.rxns,[presBac{i,1} '_'],length(presBac{i,1})+1));%finding indixes of specific reactions
+        thisBac   = presBac{i,1};               
+        rxns      = pruned_model.rxns;
+
+        % start with all reactions for this bacterium prefix
+        mask = strncmp(rxns, [thisBac '_'], length(thisBac)+1);
+
+        % Find "child" bacteria whose names extend this one
+        allBacs   = presBac(:,1);
+        childMask = strncmp(allBacs, [thisBac '_'], length(thisBac)+1);
+        childNames = allBacs(childMask);
+
+        % exclude reactions belonging to any child bacterium
+        for c = 1:numel(childNames)
+            child = childNames{c};
+            maskChild = strncmp(rxns, [child '_'], length(child)+1);
+            mask = mask & ~maskChild;
+        end
+
+        % final indices
+        matInd2 = find(mask);
+        pruned_model.rxns(matInd2)
         % merge the C matrix
         pruned_model.C(matInd1,matInd2) = couplingMatrixRed{i,1};
 

src/analysis/persephone/additionalFunctions/interrogateWBmodelsQP.m

@@ -0,0 +1,80 @@
+function interrogateWBmodelsQP(directory,resPath, solver, param)
+% Performs FBA on a all whole-body models in a folder with the quadratic flux minimisation
+% algorithm (QP) and saves the QP FBA results in a separate results folder.
+%
+% USAGE:
+%               interrogateWBmodelsQP(directory,resPath,solver)
+% 
+%
+% INPUTS
+% directory     [char] Path to folder with WBMs
+% resPath       [char] Path to location of FBA results
+% solver        [char] Solver name, e.g., gurobi.
+%
+% OPTIONAL INPUTS:
+% param         [struct] FBA parameters. See OptimizeWBModel.m or
+%               OptimizeCbModel.m for more information. All FBA parameters are set to
+%               their defaults except for param.minNorm (1e-6) and secondsTimeLimit (500
+%               seconds instead of 100 seconds)
+%
+% AUTHOR:
+% - Tim Hensen, January 2026.
+
+
+if nargin<4
+    % Set FBA parameters
+    param.minNorm = 1e-6;
+    param.secondsTimeLimit = 500;
+end
+
+% Set QP solver
+changeCobraSolver(solver,'QP',-1)
+
+% Get model names
+modelNames = what(directory).mat;
+modelPaths = fullfile(directory,modelNames);
+
+% Create output folder if not present already
+if ~isfolder(resPath)
+    mkdir(resPath)
+end
+
+% Remove already analysed models
+prevSol = what(resPath);
+if ~isempty(prevSol)
+    prevSol = prevSol.mat;
+    [~,idx] = setdiff(modelNames,prevSol);
+    modelPaths = modelPaths(idx);
+end
+
+for i=1:numel(modelPaths)
+
+    % load model
+    disp(append('load and interrogate model : ', modelNames{i}))
+    model = loadPSCMfile(modelPaths{i});
+
+    % Set objective at Whole_body_objective_rxn
+    model = changeObjective(model, 'Whole_body_objective_rxn');
+
+    % Fix objective flux bounds at one
+    model = changeRxnBounds(model,'Whole_body_objective_rxn',1,'b');
+
+    % Minimise the Euclidean norm of all reactions for a fixed objective
+    model.osenseStr = 'min';
+
+    tic
+    % Perform FBA
+    FBA = optimizeWBModel(model, param);
+    toc
+
+    % Append metabolites and reactions
+    FBA.rxns = model.rxns;
+    FBA.mets = model.mets;
+
+    % Save results
+    filePath=fullfile(resPath, append('qpFBA_',modelNames{i}));
+    solution = FBA;
+    save(filePath,'-struct', 'solution')
+end
+
+end