Welcome to the Metabolic Media Library, a community-driven repository dedicated to standardizing culture media definitions for genome-scale metabolic modeling. This project provides a curated collection of media formulations mapped to widely used human metabolic models (Recon3D and Human-GEM).
Each medium is defined as a .tsv file with the following columns:
| Metabolite_Name | Mets_HumanGEM | ExRxns_HumanGEM | Mets_Recon3D | ExRxns_Recon3D | Concentration_M |
|---|---|---|---|---|---|
| glucose | MAM01965e | MAR09034 | glc_D[e] | EX_glc_D[e] | 0.010011 |
Note
- All concentrations are in molar units (M).
- Missing entries can be left blank but the format must be respected.
- Whenever possible, include identifiers for both models to maximize interoperability.
We welcome contributions of new media formulations or improvements to existing ones.
- Copy the template file.
- Rename it appropriately (e.g.,
RPMI1640.tsv). - Fill in all relevant fields:
- Include both Recon3D and Human-GEM identifiers whenever possible.
- Submit a pull request including:
- The completed
.tsvfile in themedia/directory. - (Optional) A reference or note describing the source of concentrations
- The completed
| Model | Description | Source |
|---|---|---|
| Human-GEM | An open, community-maintained human metabolic model. | Human-GEM on GitHub |
| Recon3D | A comprehensive human metabolic model with metabolite structures and gene-protein-reaction (GPR) associations. | VMH - Recon3D |
| Toolbox | Language | Description | Installation / Docs |
|---|---|---|---|
| COBREXA.jl | Julia | Scalable metabolic modeling in Julia | COBREXA.jl Docs |
| COBRApy | Python | Python implementation of the COBRA Toolbox | COBRApy Docs |
| COBRA Toolbox | MATLAB | Original MATLAB-based framework for constraint-based modeling | COBRA Toolbox GitHub |
| RAVEN Toolbox | MATLAB | Reconstruction, Analysis and Visualization of Metabolic Networks | RAVEN Toolbox GitHub |
The composition of culture media strongly influences predictions in constraint-based metabolic models. Standardizing these definitions enables:
- Reproducibility of published simulation results
- Transparency in modeling assumptions
- Comparability across studies, models, and experimental conditions
We provide code example for integrating medium files into models using COBREXA.jl
Important
The media formulations provided can often be too restrictive and lack certain metabolites crucial for the cells growth beyond a given rate. To compensate for these missing metabolites, it is recommended to use a gapfilling solution (see documentation).
Feedback is highly appreciated. If you encounter issues, have suggestions, or would like to propose new features, please open an issue or submit a pull request.
This project builds upon the work of the metabolic modeling community. A significant portion of the initial work, particularly on media composition analysis, was carried out by Claude Haan.
This project is licensed under the MIT License.