RBC-GEM: Genome-scale metabolic model for the erythrocyte of Homo sapiens

Citation

If you use RBC-GEM in your research, please cite the following:

Haiman ZB, Key A, D'Alessandro A, Palsson BO. RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell. PLoS Comput Biol. 2025 Mar 12;21(3):e1012109. doi: 10.1371/journal.pcbi.1012109. PMID: 40072998; PMCID: PMC11925312.

All the releases are also archived in Zenodo from which specific version can be cited if used.

Keywords

Utilisation: experimental data reconstruction; multi-omics integrative analysis; model template Field: metabolic-network reconstruction Type of model: reconstruction; curated Model source: iAB-RBC-283, Human-GEM Omic source: genomics; proteomics; metabolomics; lipidomics Taxonomic name: Homo sapiens Taxonomy ID: taxonomy:9606 Metabolic system: general metabolism Tissue: Blood Cell type: Red Blood Cell (erythrocyte) Condition: generic metabolism

Installation

With Python

The recommended method is to install rbc_gem_utils is to use pip to install the software. It is recommended to do this inside a virtual environment. If you have conda, follow the instructions for managing environments

1. Clone the main branch of this repository, or download the latest release.

2. Navigate to the code directory containing the pyproject.toml file and install the package:

   cd "/my/path/RBC-GEM/code"
   pip install "."
   

3. Test your install:

    python -c "from rbc_gem_utils import show_versions; show_versions()"
   

Contributing

Contributions are always welcome! Please read the contributing guideline to get started.

Contributors

Code contributors are reported automatically by GitHub under Contributors, while other contributions come in as Issues.