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COBRApy

Maintainer K-Dense Inc. · Last updated April 1, 2026

COBRApy is a Python library for constraint-based reconstruction and analysis (COBRA) of metabolic models, essential for systems biology research. Work with genome-scale metabolic models, perform computational simulations of cellular metabolism, conduct metabolic engineering analyses, and predict phenotypic behaviors.

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Original source

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/cobrapy

Maintainer: K-Dense Inc.
License: GPL-2.0 license
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

COBRApy is a Python library for constraint-based reconstruction and analysis (COBRA) of metabolic models, essential for systems biology research. Work with genome-scale metabolic models, perform computational simulations of cellular metabolism, conduct metabolic engineering analyses, and predict phenotypic behaviors.
model = load_model("textbook") # E. coli core model model = load_model("ecoli") # Full E. coli model model = load_model("salmonella").

Source Doc

Excerpt From SKILL.md

Core Capabilities

COBRApy provides comprehensive tools organized into several key areas:

1. Model Management

Load existing models from repositories or files:

from cobra.io import load_model

## Load from files

from cobra.io import read_sbml_model, load_json_model, load_yaml_model
model = read_sbml_model("path/to/model.xml")
model = load_json_model("path/to/model.json")
model = load_yaml_model("path/to/model.yml")
python
from cobra.io import write_sbml_model, save_json_model, save_yaml_model
write_sbml_model(model, "output.xml")  # Preferred format
save_json_model(model, "output.json")  # For Escher compatibility
save_yaml_model(model, "output.yml")   # Human-readable