1,011 strain-specific models

The 1,011 strain-specific models matching Lu et al. (2019) are available from Zenodo.

panYeast-GEM: The pan-genome metabolic model of Saccharomyces cerevisiae

• Brief Model Description:

This repository contains the pan-genome metabolic model of Saccharomyces cerevisiae. This README.md is mostly copied from yeast-GEM.

• Model KeyWords: redefine GEM Category: Species; Utilisation: predictive simulation, multi-omics integrative analysis, in silico strain design, model template; Field: metabolic-network reconstruction; Type of Model: curated, reconstruction; Model Source: Yeast 7.6; Taxonomy: Saccharomyces cerevisiae; Metabolic System: General Metabolism; Condition: aerobic, glucose-limited, defined media, maximization of growth.

• Last update: 2018-06-28

• Main Model Descriptors:

This repository is administered by xx (@xx), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.

Installation

Required Software - User:

Copied from yeast-GEM

• Matlab user:
  • A functional Matlab installation (MATLAB 7.3 or higher).
  • The COBRA toolbox for MATLAB.
• Python user:
  • Python 2.7, 3.4, 3.5 or 3.6
  • cobrapy

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.
• For contributors: Fork it to your Github account, and create a new branch from devel.

Usage

Explain how strain specific models can be generated

Model Files

Include explanation that a yeast-GEM derived pan-submodel and a non-S288c pan-submodel are kept separately (with the first one being automatically generated from yeast-GEM), while the final pan model combines these two submodels 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.

Complementary Scripts

Should include following Matlab scripts:

• Convert yeast-GEM to pan-submodel
• Combine pan-submodels into one pan-model
• Generate strain specific models from pan-model and table matching genes with panIDs
• Potential gap-filling to result in a functional model

Complementary Data

Should include the following:

• Pan-genome data, matching panIDs with strain specific gene IDs

Contributors

• Eduard J. Kerkhoven (@edkerk), Chalmers University of Technology, Sweden
• Feiran Li (@feiranl), Chalmers University of Technology, Sweden
• Hongzhong Lu (@hongzhonglu), Chalmers University of Technology, Sweden
• Benjamín J. Sánchez (@BenjaSanchez), Chalmers University of Technology, Sweden