Merge pull request #365 from SysBioChalmers/develop

GECKO 3.1.3

README.md

@@ -4,24 +4,24 @@
 [![GitHub Discussions](https://img.shields.io/github/discussions-search?query=repo%3Asysbiochalmers%2Fgecko&label=GitHub%20Discussions)](https://github.com/SysBioChalmers/GECKO/discussions)
 [![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.7699818.svg)](https://doi.org/10.5281/zenodo.7699818)
 
-## About GECKO 3
+## About GECKO 3.0
 
 The **GECKO** toolbox enhances a **G**enome-scale model to account for **E**nzyme **C**onstraints, using **K**inetics and **O**mics. The resulting enzyme-constrained model (**ecModel**) can be used to perform simulations where enzyme allocation is either drawn from a total protein pool, or constrained by measured protein levels from proteomics data.
 
-
 💡 In the [`GECKO/tutorials`](https://github.com/SysBioChalmers/GECKO/tree/main/tutorials) folder there are examples of how GECKO can be applied to GEMs, in either of its _full_ or _light_ forms. Each `protocol.m` contains instructions on how to reconstruct and analyze an ecModel, demonstrating how different fuctions in GECKO can be used. These two scripts complement the [protocols paper](#citation).
 
 _**Note:** Regarding code and model compatibility with earlier GECKO versions, see [Previous versions: GECKO 1 and 2](https://github.com/SysBioChalmers/GECKO/wiki/Previous-versions:-GECKO-1-and-2)_.
 
+## Cite us
+
+If you have used GECKO in your work, please cite:
+
+> Chen Y, Gustafsson J, Tafur Rangel A, Anton M, Domenzain I, Kittikunapong C, Li F, Yuan L, Nielsen J, Kerkhoven EJ. Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0. Nature Protocols. 2024 Jan 18:1-39. doi: [10.1038/s41596-023-00931-7](https://doi.org/10.1038/s41596-023-00931-7)
 
 ## Documentation
 **Installation instructions** and other information is available in the **[Wiki](https://github.com/SysBioChalmers/GECKO/wiki)**. The source code documentation is also available 
 [online](http://sysbiochalmers.github.io/GECKO/doc/). Use [GitHub Discussions](https://github.com/SysBioChalmers/GECKO/discussions) for support, to ask questions or leave comments.
 
-## Citation
-
-- The GECKO 3 publication is in press at Nature Protocols. Once published, citation information will appear here.
-
 ## Contributing
 
 Contributions are always welcome! Please read the [contributing guidelines](https://github.com/SysBioChalmers/GECKO/blob/main/.github/CONTRIBUTING.md) to get started.

src/geckomat/gather_kcats/runDLKcat.m

@@ -31,7 +31,7 @@ function runDLKcat(modelAdapter)
 % Check if Docker is installed
 [checks.docker.status, checks.docker.out] = system('docker --version');
 if checks.docker.status ~= 0
-    error('Cannot find Docker. Make sure it is installed.')
+    error('Cannot find Docker, make sure it is installed. If it is, it might be required to start Matlab from the command-line instead of the launcher in order for Docker to be detected and used.')
 end
 
 disp('Running DLKcat prediction, this may take many minutes, especially the first time.')

src/geckomat/utilities/saveEcModel.m

@@ -40,12 +40,12 @@ function saveEcModel(ecModel,filename,modelAdapter)
 
 switch filename(end-3:end)
     case {'.xml','sbml'}
-        exportModel(ecModel,[filename '.xml']);
+        exportModel(ecModel, filename);
         %Convert notation "e-005" to "e-05 " in stoich. coeffs. to avoid
         %inconsistencies between Windows and MAC:
-        copyfile([filename '.xml'],'backup.xml')
+        copyfile(filename,'backup.xml')
         fin  = fopen('backup.xml', 'r');
-        fout = fopen([filename '.xml'], 'w');
+        fout = fopen(filename, 'w');
         still_reading = true;
         while still_reading
             inline = fgets(fin);

tutorials/full_ecModel/protocol.m

@@ -1,4 +1,4 @@
-% This file accompanies the GECKO3 Nature Protocols paper (DOI TO BE ADDED).
+% This file accompanies the GECKO 3 Nature Protocols paper https://doi.org/10.1038/s41596-023-00931-7.
 %
 % The function of this script is to demonstrate the reconstruction and
 % analysis of a *full* ecModel. As example, it here uses the yeast-GEM

tutorials/light_ecModel/protocol.m

@@ -1,4 +1,4 @@
-% This file accompanies the GECKO3 Nature Protocols paper (DOI TO BE ADDED).
+% This file accompanies the GECKO 3 Nature Protocols paper https://doi.org/10.1038/s41596-023-00931-7.
 %
 % The function of this script is to demonstrate the reconstruction and
 % analysis of a *full* ecModel. As example, it here uses the yeast-GEM
@@ -74,7 +74,7 @@
 % STEP 26 Merge BRENDA and DLKcat derived values
 kcatList_merged = mergeDLKcatAndFuzzyKcats(kcatList_DLKcat, kcatList_fuzzy);
 
-% STEP 27 Implement kcat avlues into model.ec.kcat
+% STEP 27 Implement kcat values into model.ec.kcat
 ecModel = selectKcatValue(ecModel,kcatList_merged);
 
 % STEP 28
@@ -96,7 +96,7 @@
 % -standardMW/standardKcat as the stoiciometric coefficient.
 [ecModel, rxnsMissingGPR, standardMW, standardKcat] = getStandardKcat(ecModel);
 
-% STEP 31 Apply kcat avlues to S-matrix
+% STEP 31 Apply kcat values to S-matrix
 % In light ecModels the kcat values are also kept in ecModels.ec.kcat, and
 % only after running applyKcatConstraints are these introduced in the
 % ecModel.S matrix. In constrast to full ecModels, the applyKcatConstraints