cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
npx skills add LeonChaoX/qinyan-academic-skills --skill cobrapy --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# COBRApy - Constraint-Based Reconstruction and Analysis ## Overview 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. ## Core Capabilities COBRApy provides comprehensive tools organized into several key areas: ### 1. Model Management Load existing models from repositories or files: ```python from cobra.io import load_model # Load bundled test models model = load_model("textbook") # E. coli core model model = load_model("ecoli") # Full E. coli model model = load_model("salmonella") # 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") ``` Save models in various formats: ```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
- Overview
- Core Capabilities
- 1. Model Management
- 2. Model Structure and Components
- 3. Flux Balance Analysis (FBA)
- 4. Flux Variability Analysis (FVA)
- 5. Gene and Reaction Deletion Studies
- 6. Growth Media and Minimal Media
- 7. Flux Sampling
- 8. Production Envelopes
- 9. Gapfilling
- 10. Model Building
- Common Workflows
- Workflow 1: Load Model and Predict Growth
What does the cobrapy skill do?
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill cobrapy --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.