https://github.com/sysbiochalmers/kluyveromyces_marxianus-gem
The consensus GEM for Kluyveromyces marxianus
https://github.com/sysbiochalmers/kluyveromyces_marxianus-gem
genome-scale-models kluyveromyces-marxianus systems-biology
Last synced: 2 months ago
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The consensus GEM for Kluyveromyces marxianus
- Host: GitHub
- URL: https://github.com/sysbiochalmers/kluyveromyces_marxianus-gem
- Owner: SysBioChalmers
- License: cc-by-4.0
- Created: 2017-11-22T15:06:01.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2020-02-25T11:12:26.000Z (over 5 years ago)
- Last Synced: 2025-01-30T22:51:19.396Z (4 months ago)
- Topics: genome-scale-models, kluyveromyces-marxianus, systems-biology
- Language: MATLAB
- Homepage: https://github.com/SysBioChalmers/Kluyveromyces_marxianus-GEM
- Size: 3.79 MB
- Stars: 2
- Watchers: 5
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: history.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
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README
# Kluyveromyces_marxianus-GEM: The consensus genome-scale metabolic model of _Kluyveromyces marxianus_
[](https://badge.fury.io/gh/sysbiochalmers%2Fkluyveromyces_marxianus-gem) [](https://gitter.im/SysBioChalmers/Kluyveromyces_marxianus-GEM?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
* Brief Model Description:
This repository contains the current consensus genome-scale metabolic model of the ascomycetous yeast _Kluyveromyces marxianus_, named **Kluyveromyces_marxianus-GEM**. The model contains 4 compartments: extracellular, cytosol, mitochondrion and endoplasmic reticulum. For the latest release please [click here](https://github.com/SysBioChalmers/Kluyveromyces_marxianus-GEM/releases).
* Model KeyWords:
**GEM Category:** species; **Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** reconstruction, curated; **Model Source:** iOD907, [yeast-GEM](https://github.com/SysBioChalmers/yeast-GEM); **Omic Source:** genomics; **Taxonomy:** _Kluyveromyces marxianus_; **Metabolic System:** general metabolism; **Bioreactor**; **Strain;** **Condition:** aerobic, glucose-limited, defined media;
* Last update: 2019-11-16
* Main Model Descriptors:
|Taxonomy | Template Model | Reactions | Metabolites| Genes |
|:-------:|:--------------:|:---------:|:----------:|:-----:|
|_Kluyveromyces marxianus_|iOD907|1913|1531|996|
This repository is administered by Simonas Marcišauskas ([@simas232](https://github.com/simas232)), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.
## Installation
### Required Software - User:
* MATLAB user:
* A functional MATLAB installation (2016b or higher)
* The [COBRA Toolbox for MATLAB](https://github.com/opencobra/cobratoolbox)
* Python user:
* Python 2.7, 3.4, 3.5 or 3.6
* [cobrapy](https://github.com/opencobra/cobrapy)
### Required Software - Contributor:
* Both of the previous MATLAB requirements
* The [RAVEN Toolbox for MATLAB](https://github.com/SysBioChalmers/RAVEN)
* A [git wrapper](https://github.com/manur/MATLAB-git) added to the search path
### Dependencies - Recommended Software:
* For MATLAB, the [libSBML MATLAB API](https://sourceforge.net/projects/sbml/files/libsbml/MATLAB%20Interface/) (version 5.17.0 is recommended)
* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations
### Installation Instructions
* For users: Clone it from [`master`](https://github.com/SysBioChalmers/Kluyveromyces_marxianus-GEM) in the GitHub repo, or just download [the latest release](https://github.com/SysBioChalmers/Kluyveromyces_marxianus-GEM/releases)
* For contributors: Fork it to your GitHub account, and create a new branch from [`devel`](https://github.com/SysBioChalmers/Kluyveromyces_marxianus-GEM/tree/devel)
## Usage
Make sure to load/save the model with the corresponding wrapper functions!
* In MATLAB:
* Loading: `code/loadKmxModel.m`
* Saving: `code/saveKmxModel.m`
* In Python:
* Loading: `code/loadKmxModel.py`
* Saving: currently unavailable
## Model Files
The model is available in `.xml`, `.txt`, `.yml`, `.mat` and `.xlsx` (the last 2 extensions only in `master`). Additionally, the following 2 files are available:
* `dependencies.txt`: Tracks versions of toolboxes & SBML used for saving the model.
* `boundaryMets.txt`: Contains a list of all boundary metabolites in model, listing the id and name.
### Complementary Code
* `missingFields`: Folder with functions for adding missing fields to the model.
* `modelCuration`: Folder with curation functions.
* `otherChanges`: Folder with other types of changes.
* `increaseKmxVersion.m`: Updates the version of the model in `version.txt` and as metaid in the `.xml` file. Saves the model as `.mat` and as `.xlsx`
* `loadKmxModel.m`: Loads the yeast model from the `.xml` file for MATLAB.
* `loadKmxModel.py`: Loads the yeast model from the `.xml` file for Python.
* `saveKmxModel.m`: Saves yeast model as a `.xml`, `.yml` and `.txt` file, and updates `boundaryMets.txt` and `dependencies.txt`.
### Complementary Data
* `biomassComposition`: The detailed information about the biomass composition considered in the model.
* `proteome`: The list of all proteins for DMKU3-1042 strain. Useful when one wants to convert _K. marxianus_ genes to _S. cerevisiae_ and perform gene knockout simulations.
## Citation
>Marcišauskas S, Ji B, Nielsen J (2019). Reconstruction and analysis of a _Kluyveromyces marxianus_ genome-scale metabolic model. BMC Bioinformatics 20:551. doi:[10.1186/s12859-019-3134-5](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3134-5)
## Contributing
Contributions are always welcome! Please read the [contributions guideline](https://github.com/SysBioChalmers/Kluyveromyces_marxianus-GEM/blob/master/.github/CONTRIBUTING.md) to get started.
## Contributors
* [Simonas Marcišauskas](https://www.chalmers.se/en/Staff/Pages/simmarc.aspx) ([@simas232](https://github.com/simas232)), Chalmers University of Technology, Sweden
## More from SysBio Chalmers
For more recently published genome-scale models and systems biology related software from the Systems and Synthetic Biology group at Chalmers University of Technology, please visit the [GitHub page](https://github.com/SysBioChalmers). For more information and publications by the Systems and Synthetic Biology please visit [SysBio](https://www.sysbio.se/).