yeast-GEM: The consensus genome-scale metabolic model of Saccharomyces cerevisiae

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;

Last update: 2020-09-18
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.

Installation

Required Software - User:

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

Required Software - Contributor:

Both of the previous Matlab requirements.
The RAVEN toolbox for MATLAB.
A git wrapper added to the search path.

Dependencies - Recommended Software:

For Matlab, the libSBML MATLAB API (version 5.17.0 is recommended).
Gurobi Optimizer for any simulations.

Installation Instructions

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.

Usage

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

Online Visualization/Simulation

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.

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.

Citation

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.
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.

Contributing

Contributions are always welcome! Please read the contributions guideline to get started.

qi1225/yeast-GEM