Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

GECKO 3.2.2 #388

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
+192 −148
Open

GECKO 3.2.2 #388

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 6 additions & 4 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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.
Expand All @@ -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
Expand Down
3 changes: 1 addition & 2 deletions doc/src/geckomat/change_model/applyKcatConstraints.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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>
</body>
</html>
2 changes: 1 addition & 1 deletion doc/src/geckomat/change_model/setKcatForReactions.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
Loading
Loading