https://github.com/sysbiochalmers/ecoli-gem

Genome-scale metabolic model for Escherichia coli
https://github.com/sysbiochalmers/ecoli-gem

genome-scale-models standard-gem systems-biology

Last synced: 4 months ago
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Genome-scale metabolic model for Escherichia coli

• Host: GitHub
• URL: https://github.com/sysbiochalmers/ecoli-gem
• Owner: SysBioChalmers
• License: cc-by-4.0
• Created: 2025-02-06T09:40:53.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-09-01T14:46:15.000Z (10 months ago)
• Last Synced: 2025-09-01T16:37:03.215Z (10 months ago)
• Topics: genome-scale-models, standard-gem, systems-biology
• Language: HTML
• Homepage: https://sysbiochalmers.github.io/Ecoli-GEM/
• Size: 8.95 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE.md
  • Code of conduct: .github/CODE_OF_CONDUCT.md

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README

          
## Ecoli-GEM: Genome-scale metabolic model for Escherichia coli

[![Version](https://badge.fury.io/gh/SysBioChalmers/Ecoli-GEM.svg)](https://badge.fury.io/gh/sysbiochalmers/Ecoli-GEM)  

[![Zenodo](https://zenodo.org/badge/{{Zenodo ID}}.svg)](https://zenodo.org/badge/latestdoi/{{Zenodo ID}})  

[![Gitter chat](https://badges.gitter.im/SysBioChalmers/Ecoli-GEM.svg)](https://gitter.im/SysBioChalmers)

#### Description

This repository contains the latest version the Ecoli-GEM, a genome scale metabolic model of _Escherichia coli str. K-12 substr. MG1655_. 

#### Citation

The latest version of the E. coli GEM, iML1515, was taken from BiGG Models with the following publication:

  > Monk, J.M., Lloyd, C.J., Brunk, E. et al (2017). iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol 35, 904–908 [doi:10.1038/nbt.3956](https://doi.org/10.1038/nbt.3956)

#### Keywords

**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:** [EscherichiaColi](https://doi.org/10.1038/nbt.3956)   

**Omic source:** {{ genomics; metabolomics }}  

**Taxonomic name:** _Escherichia coli str. K-12 substr. MG1655_   

**Taxonomy ID:** [taxonomy:511145](https://identifiers.org/taxonomy:511145)   

**Genome ID:** [insdc.gca:GCA_000005845.2](https://identifiers.org/insdc.gca:GCA_000005845.2)   

**Metabolic system:** {{ general metabolism }}  

**Cell type:** Prokaryotic 

**Strain:** MG1655  

**Condition:** {{ aerobic; glucose-limited; defined media }}  

### Installation

{{ Be mindful of users who do not have a typical background - provide a clear overview of the required software. Also, there might be different requirements for users and collaborators. }}

### Usage

{{ Describe how to load and save the model. }}

### Contributing

Contributions are always welcome! Please read the [contributing guideline](.github/CONTRIBUTING.md) to get started.

### Contributors

Code contributors are reported automatically by GitHub under [Contributors](https://github.com/SysBioChalmers/Ecoli-GEM/graphs/contributors), while other contributions come in as [Issues](https://github.com/SysBioChalmers/Ecoli-GEM/issues).