Salb-GEM-v1.1(Biosustain) is a genome-scale metabolic model (GEM) reconstructed for Streptomyces albus J1074, based on original version of Salb-GEM and phenomics data from DTU Biosustain. This model enables in silico simulations of metabolic fluxes under diverse conditions, supporting applications in:
- 🧬 Systems biology (multi-omics integration, phenotype prediction)
- 🧪 Biotechnology (strain engineering, substrate utilization)
- 🧠 Basic research (gene essentiality, metabolic pathway analysis)
| Property | Value | Description |
|---|---|---|
| Taxonomy | salb | Streptomyces albus J1074 |
| Latest Update | 2025-07-13 | |
| Version | 1.1 | |
| Reactions | 2274 | |
| Metabolites | 1888 | |
| Genes | 1405 |
git clone https://github.com/biosustain/Salb-GEM-Biosustain.gitfrom cobra.io import load_json_model
model = load_json_model("./model/Salb-GEM-v1.1(Biosustain).json") root
├── model
│ └── Salb-GEM-Biosustain.xml: The metabolic model in SBML format
│ └── Salb-GEM-Biosustain.yml: The metabolic model in YAML format
│ └── Salb-GEM-Biosustain.json: The metabolic model in JSON format
│ └── Salb-GEM-Biosustain.mat: The metabolic model in MatLab format
└── notebooks: Model curation workflow
│ └── 1.phenomics: Create evaluation metrics using phenomics data
│ └── 2.gapfilling: Gapfill Salb-GEM model using various gapfilling techniques
│ └── 3.pathway_engineering: Engineer PTA pathway into the gapfilled Salb-GEM
│ └── 4.medium_optimization: Using engineered PTA pathway model for medium optimization
│ └── 5.paper: Figure creation for publication
└── data: External Data used for gapfilling and manual curation
│ └── external: Genomics scale models and name matching files for gapfilling
│ └── interim: Files generated from gapfilling
│ └── raw: Pheomics and fermentation data
The model has been validated against:
All model releases will be archived on Zenodo.
Contributions are welcome! Please read our contributing guidelines before submitting issues or pull requests.
