feat: keep track of kcat curations (#385)

* doc: README.md MATLAB badge

* fix: setKcatForReactions correct source field

* feat: sensitivityTuning note of preTuneKcat

* doc: adapterTemplate set reviewed to false

by default allow for more uniprot protein matches

* fix: update tutorial ecYeastGEM.yml

* doc: clarify params.enzyme_comp in model adapter

README.md

@@ -1,14 +1,16 @@
 <img src="./GECKO.png" width="200px">
 
-![Current version](https://badge.fury.io/gh/sysbiochalmers%2Fgecko.svg)
+[![Current release](https://img.shields.io/github/release/SysBioChalmers/GECKO/all.svg)](https://GitHub.com/SysBioChalmers/GECKO/releases/)
 [![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)
+[![MATLAB File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://se.mathworks.com/matlabcentral/fileexchange/125960-gecko-toolbox)
 
-## About GECKO 3.0
+
+## About GECKO 3
 
 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).
+💡 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 [Nature Protocols](https://doi.org/10.1038/s41596-023-00931-7) paper ([**PDF**](https://drive.google.com/file/d/1_AGz6GmQPOyshfUZ6K-L2myzU43rQ6tu/view)).
 
 ### Significant changes since protocol publication
 - GECKO **3.2.0**: all protein usage reactions draw from the protein pool, even if they are constrained by proteomics data. This affects **Step 58** in the protocol, changing behaviour of `constrainEnzConcs` and making `updateProtPool` obsolete, `tutorials/full_ecModel/protocol.m` is updated to reflect this change. See [#357](https://github.com/SysBioChalmers/GECKO/issues/375) for more details.  
@@ -19,7 +21,7 @@ _**Note:** Regarding code and model compatibility with earlier GECKO versions, s
 
 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)
+> 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* **19**, 629-667 (2024). 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 

doc/src/geckomat/change_model/applyKcatConstraints.html

@@ -177,8 +177,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0115         model.S(prot_pool_idx, hasEc(i)) = -min(MWkcat/3600);
 0116     <span class="keyword">end</span>
 0117 <span class="keyword">end</span>
-0118 <span class="keyword">end</span>
-0119</pre></div>
+0118 <span class="keyword">end</span></pre></div>
 <hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
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doc/src/geckomat/change_model/setKcatForReactions.html

@@ -113,7 +113,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0047     <span class="keyword">end</span>
 0048 <span class="keyword">end</span>
 0049 ecModel.ec.kcat(rxnsToChange)   = kcat;
-0050 ecModel.ec.source(rxnsToChange) = {<span class="string">'from setKcatForReactions'</span>};
+0050 ecModel.ec.source(rxnsToChange) = {<span class="string">'setKcatForReactions'</span>};
 0051 <span class="keyword">end</span></pre></div>
 <hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>