Purpose:
“Hosting up-to-date high quality published versioned genome-scale metabolic models developed in SysBio Group”
- Up-to-date: easy access for SysBio members to the latest version of each GEM
- High Quality: contributions and curations from multiple researchers both hosted and integrated in the main model, along with Documentation
- Versioned: previous versions of the same model - visualisation of the computational and scientific progress
The repository contains:
-
A folder called ModelFiles. It includes the current genome-scale metabolic model of Saccharomyces cerevisiae used in the @SysBioChalmers group. It is an improved version of the consensus metabolic model, version 7.6. The formats that the model is available are :
- mat
- txt
- xls
- xml
- yaml
The model:
| Taxonomy | Template Model | Reactions | Metabolites | Genes |
|---|---|---|---|---|
| Saccharomyces cerevisiae | Yeast 7.6 | 3496 | 2224 | 909 |
- A folder called ComplementaryScripts. It contains:
- MATLAB-git-master folder, required fir the proper use of the YeastMetaboliNetwork-GEM
- YeastMetabolicNetwork-GEMComplementaryScripts folder, includes all the scripts from the YeastMetabolicNetwork-GEM repository
- WorkshopScript.m, a matlab script that includes all the GEM manipulation commands for this workshop
Instructions for the workshop can be found here
This repository is administered by Dimitra Lappa, demilappa, Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology
Last update: 2018-03-22
- PROGRAMMING LANGUAGE/Version (e.g.):
- You need a functional Matlab installation of Matlab_R_2011_Rb (MATLAB 7.3 and higher)
- The COBRA toolbox for MATLAB. An up-to-date version from COBRA GitHub repository is strongly recommended . Add the directory to your Matlab path, instructions here
- The RAVEN toolbox for MATLAB. An up-to-date version from RAVEN GitHub repository is strongly recommended . Add the directory to your Matlab path, instructions here
- libSBML MATLAB API (version 5.14.0 is recommended).
- Clone gem-workshop branch from SysBioChalmers GitHub
- Add the directory to your Matlab path, instructions here
- Dimitra Lappa, Chalmers University of Technology, Gothenburg Sweden
- Mihail Anton, Chalmers University of Technology, Gothenburg Sweden
Contributors for the Yeast Repository:
- Eduard J. Kerkhoven (@edkerk), Chalmers University of Technology, Gothenburg Sweden
- Feiran Li (@feiranl), Chalmers University of Technology, Gothenburg Sweden
- Hongzhong Lu (@hongzhonglu), Chalmers University of Technology, Gothenburg Sweden
- Simonas Marcišauskas (@simas232), Chalmers University of Technology, Gothenburg Sweden
- Benjamín J. Sánchez (@BenjaSanchez), Chalmers University of Technology, Gothenburg Sweden