- Brief Model Description:
This repository contains the current consensus genome-scale metabolic model of Saccharomyces cerevisiae. It is the continuation of the legacy project yeastnet. For the latest release please click here.
- 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: YeastMetabolicNetwork; Omic Source: genomics, metabolomics; Taxonomy: Saccharomyces cerevisiae; Metabolic System: general metabolism; Bioreactor; Strain: S288C; Condition: aerobic, glucose-limited, defined media;
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Last update: 2020-09-18
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Main Model Descriptors:
Taxonomy | Template Model | Reactions | Metabolites | Genes |
---|---|---|---|---|
Saccharomyces cerevisiae | Yeast 7.6 | 4058 | 2742 | 1150 |
This repository is administered by Benjamín J. Sánchez (@BenjaSanchez), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.
- Matlab user:
- A functional Matlab installation (MATLAB 7.3 or higher).
- The COBRA toolbox for MATLAB.
- Python user: Python 3.4, 3.5, 3.6 or 3.7
- Both of the previous Matlab requirements.
- The RAVEN toolbox for MATLAB.
- A git wrapper added to the search path.
- For Matlab, the libSBML MATLAB API (version 5.17.0 is recommended).
- Gurobi Optimizer for any simulations.
- For users: Clone it from
master
in the Github repo, or just download the latest release. If you work in python, please create an environment with all requirements:pip install -r requirements/requirements.txt # installs all dependencies touch .env # creates a .env file for locating the root
- For contributors: Fork it to your Github account, and create a new branch from
devel
.
Make sure to load/save the model with the corresponding wrapper functions!
- In Matlab:
cd ./ComplementaryScripts model = loadYeastModel(); % loading saveYeastModel(model); % saving
- In Python:
import ComplementaryScripts.io as io model = io.read_yeast_model() # loading io.write_yeast_model(model) # saving
- You can visualize selected pathways of yeast-GEM and perform online constraint-based simulations using Caffeine, by creating a simulation with the latest yeast-GEM version available, and choosing any S. cerevisiae map (currently only
iMM904
maps are available). Learn more about Caffeine. - Additionally, you can interactively navigate model components and visualize 3D representations of all compartments and subsystems of yeast-GEM at Metabolic Atlas. Learn more about Metabolic Atlas.
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.
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If you use yeast-GEM please cite the yeast8 paper:
Lu, H. et al. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications 10, 3586 (2019). https://doi.org/10.1038/s41467-019-11581-3.
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Additionally, all yeast-GEM releases are archived in Zenodo, for you to cite the specific version of yeast-GEM that you used in your study, to ensure reproducibility. You should always cite the original publication + the specific version, for instance:
The yeast consensus genome-scale model [Lu et al. 2019], version 8.3.4 [Sánchez et al. 2019], was used.
Find the citation details for your specific version here.
Contributions are always welcome! Please read the contributions guideline to get started.