https://github.com/sysbiochalmers/salb-gem
GEM for Streptomyces albidoflavus (S.albus J1074)
https://github.com/sysbiochalmers/salb-gem
Last synced: over 1 year ago
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GEM for Streptomyces albidoflavus (S.albus J1074)
- Host: GitHub
- URL: https://github.com/sysbiochalmers/salb-gem
- Owner: SysBioChalmers
- License: cc-by-4.0
- Created: 2019-03-26T08:07:46.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2021-04-21T17:47:13.000Z (about 5 years ago)
- Last Synced: 2025-01-30T22:51:19.321Z (over 1 year ago)
- Language: MATLAB
- Homepage:
- Size: 30.7 MB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
## Salb-GEM: genome-scale metabolic model for _Streptomyces albus_ J1074
[](https://badge.fury.io/gh/SysBioChalmers%2FSalb-GEM) [](https://zenodo.org/badge/latestdoi/177741819) [](https://gitter.im/SysBioChalmers/Salb-GEM)
#### Brief Model Description
This repository entails the genome-scale metabolic model (GEM) SalbGEM for *Streptomyces albidoflavus*, previously and more commonly recognized under the name *S. albus J1074*.
#### Organism Information
*S. albus* J1074 is recognized as an effective host for heterologous production of natural products and secondary metabolites. Its fast growth and an efficient genetic system based on a naturally minimized genome have been attributed for the strain's advantage in expression of biosynthetic pathways for a variety of natural products including antibiotics and flavonoids ([Zaburannyi et al., 2014](https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-97), [Marin et al., 2017](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0207278)).
#### Main Model Descriptors:
|Taxonomy | Template Model | Reactions | Metabolites| Genes |
|:-------:|:--------------:|:---------:|:----------:|:-----:|
|_Streptomyces albus J1074_|[Sco-GEM](https://github.com/SysBioChalmers/Sco-GEM)|2231|1872|1381|
This repository is administered by Cheewin Kittikunapong, Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.
### Installation
#### Recommended Software:
* A functional Matlab installation (MATLAB 7.3 or higher).
* [RAVEN Toolbox 2](https://github.com/SysBioChalmers/RAVEN) for MATLAB (required for contributing to development).
* libSBML MATLAB API ([version 5.16.0](https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/) is recommended).
* [Gurobi Optimizer for MATLAB](http://www.gurobi.com/registration/download-reg).
#### Installation Instructions
* Clone the [master](https://github.com/SysBioChalmers/Salb-GEM) branch from [SysBioChalmers GitHub](https://github.com/SysBioChalmers).
* Add the directory to your Matlab path, instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com).
### Citation
* All model releases will be archived on [Zenodo](https://doi.org/10.5281/zenodo.3693406).
* The associated manuscript is in preparation and will be available for citations in the near future.