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Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
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Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis. 📦 Ships with scientific-agent-skills
</> SKILL.md
cobrapy.SKILL.md
---
name : cobrapy
description : Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
license : GPL-2.0 license
allowed-tools: Read Write Edit Bash
compatibility : Requires Python 3.9+ (cobra 0.30+ dropped 3.8). Install with uv pip install. GLPK (swiglpk) is the default solver; CPLEX/Gurobi optional. load_model fetches from bundled data, BiGG, or BioModels (network required for remote models).
metadata : {"version": "1.1", "skill-author": "K-Dense Inc."}
---
# 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.
**Version note:** Examples target **cobra 0.31.1** on PyPI (import `cobra`). Docs: [cobrapy.readthedocs.io](https://cobrapy.readthedocs.io/en/latest/). Repo: [opencobra/cobrapy](https://github.com/opencobra/cobrapy).
## When to Use This Skill
Use this skill when:
- Loading, building, or exporting genome-scale metabolic models (SBML, JSON, YAML)
- Running FBA, pFBA, FVA, or flux sampling on COBRA models
- Performing gene or reaction knockout screens and production envelope analysis
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- Designing or optimizing growth media and exchange constraints
- Gap-filling infeasible models or validating model consistency
## Installation
```bash
uv pip install "cobra==0.31.1"
```
MATLAB model I/O (optional):
```bash
uv pip install "cobra[array]==0.31.1"
```
COBRApy uses [optlang](https://optlang.readthedocs.io/) for solvers. GLPK installs automatically via `swiglpk`. For large MILPs/QPs, cobra 0.29+ adds a **hybrid** solver (HIGHS/OSQP); `model.solver = "osqp"` now routes through hybrid and may error on plain LPs in a future release—prefer `model.solver = "hybrid"` when available.
## 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
# Bundled locally (no network): textbook, iJO1366, salmonella
model = load_model("textbook") # alias for e_coli_core (95 reactions)
model = load_model("e_coli_core") # same core E. coli model
model = load_model("iJO1366") # genome-scale E. coli (bundled)
model = load_model("salmonella") # Salmonella iYS1720 (bundled)
# Remote (BiGG / BioModels; requires network, cached after first fetch)
model = load_model("iML1515") # E. coli genome-scale on BiGG
# 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 Escher compatibility
save_yaml_model(model, "output.yml") # Human-readable
```
### 2. Model Structure and Components
Access and inspect model components:
```python
# Access components
model.reactions # DictList of all reactions
model.metabolites # DictList of all metabolites
model.genes # DictList of all genes
# Get specific items by ID or index
reaction = model.reactions.get_by_id("PFK")
metabolite = model.metabolites[0]
# Inspect properties
print(reaction.reaction) # Stoichiometric equation
print(reaction.bounds) # Flux constraints
print(reaction.gene_reaction_rule) # GPR logic
print(metabolite.formula) # Chemical formula
print(metabolite.compartment) # Cellular location
```
### 3. Flux Balance Analysis (FBA)
Perform standard FBA simulation:
```python
# Basic optimization
solution = model.optimize()
print(f"Objective value: {solution.objective_value}")
print(f"Status: {solution.status}")
# Access fluxes
print(solution.fluxes["PFK"])
print(solution.fluxes.head())
# Fast optimization (objective value only)
objective_value = model.slim_optimize()
# Change objective
model.objective = "ATPM"
solution = model.optimize()
```
Parsimonious FBA (minimize total flux):
```python
from cobra.flux_analysis import pfba
solution = pfba(model)
```
Geometric FBA (find central solution):
```python
from cobra.flux_analysis import geometric_fba
solution = geometric_fba(model)
```
### 4. Flux Variability Analysis (FVA)
Determine flux ranges for all reactions:
```python
from cobra.flux_analysis import flux_variability_analysis
# Standard FVA
fva_result = flux_variability_analysis(model)
# FVA at 90% optimality
fva_result = flux_variability_analysis(model, fraction_of_optimum=0.9)
# Loopless FVA (eliminates thermodynamically infeasible loops)
fva_result = flux_variability_analysis(model, loopless=True)
# FVA for specific reactions
fva_result = flux_variability_analysis(
model,
reaction_list=["PFK", "FBA", "PGI"]
)
```
### 5. Gene and Reaction Deletion Studies
Perform knockout analyses:
```python
from cobra.flux_analysis import (
single_gene_deletion,
single_reaction_deletion,
double_gene_deletion,
double_reaction_deletion
)
# Single deletions
gene_results = single_gene_deletion(model)
reaction_results = single_reaction_deletion(model)
# Double deletions (uses multiprocessing)
double_gene_results = double_gene_deletion(
model,
processes=4 # Number of CPU cores
)
# Manual knockout using context manager
with model:
model.genes.get_by_id("b0008").knock_out()
solution = model.optimize()
print(f"Growth after knockout: {solution.objective_value}")
# Model automatically reverts after context exit
```
### 6. Growth Media and Minimal Media
Manage growth medium:
```python
# View current medium
print(model.medium)
# Modify medium (must reassign entire dict)
medium = model.medium
medium["EX_glc__D_e"] = 10.0 # Set glucose uptake
medium["EX_o2_e"] = 0.0 # Anaerobic conditions
model.medium = medium
# Calculate minimal media
from cobra.medium import minimal_medium
# Minimize total import flux
min_medium = minimal_medium(model, minimize_components=False)
# Minimize number of components (uses MILP, slower)
min_medium = minimal_medium(
model,
minimize_components=True,
open_exchanges=True
)
```
### 7. Flux Sampling
Sample the feasible flux space:
```python
from cobra.sampling import sample
# Sample using OptGP (default, supports parallel processing)
samples = sample(model, n=1000, method="optgp", processes=4)
# Sample using ACHR
samples = sample(model, n=1000, method="achr")
# Validate samples
from cobra.sampling import OptGPSampler
sampler = OptGPSampler(model, processes=4)
sampler.sample(1000)
validation = sampler.validate(sampler.samples)
print(validation.value_counts()) # Should be all 'v' for valid
```
### 8. Production Envelopes
Calculate phenotype phase planes:
```python
from cobra.flux_analysis import production_envelope
# Standard production envelope
envelope = production_envelope(
model,
reactions=["EX_glc__D_e", "EX_o2_e"],
objective="EX_ac_e" # Acetate production
)
# With carbon yield
envelope = production_envelope(
model,
reactions=["EX_glc__D_e", "EX_o2_e"],
carbon_sources="EX_glc__D_e"
)
# Visualize (use matplotlib or pandas plotting)
import matplotlib.pyplot as plt
envelope.plot(x="EX_glc__D_e", y="EX_o2_e", kind="scatter")
plt.show()
```
### 9. Gapfilling
Add reactions to make models feasible:
```python
from cobra.flux_analysis import gapfill
# Provide a universal reaction database (SBML/JSON); not bundled in cobra 0.31+
from cobra.io import read_sbml_model
universal = read_sbml_model("path/to/universal_reactions.xml")
# Perform gapfilling
with model:
# Remove reactions to create gaps for demonstration
model.remove_reactions([model.reactions.PGI])
# Find reactions needed
solution = gapfill(model, universal)
print(f"Reactions to add: {solution}")
```
### 10. Model Building
Build models from scratch:
```python
from cobra import Model, Reaction, Metabolite
# Create model
model = Model("my_model")
# Create metabolites
atp_c = Metabolite("atp_c", formula="C10H12N5O13P3",
name="ATP", compartment="c")
adp_c = Metabolite("adp_c", formula="C10H12N5O10P2",
name="ADP", compartment="c")
pi_c = Metabolite("pi_c", formula="HO4P",
name="Phosphate", compartment="c")
# Create reaction
reaction = Reaction("ATPASE")
reaction.name = "ATP hydrolysis"
reaction.subsystem = "Energy"
reaction.lower_bound = 0.0
reaction.upper_bound = 1000.0
# Add metabolites with stoichiometry
reaction.add_metabolites({
atp_c: -1.0,
adp_c: 1.0,
pi_c: 1.0
})
# Add gene-reaction rule
reaction.gene_reaction_rule = "(gene1 and gene2) or gene3"
# Add to model
model.add_reactions([reaction])
# Add boundary reactions
model.add_boundary(atp_c, type="exchange")
model.add_boundary(adp_c, type="demand")
# Set objective
model.objective = "ATPASE"
```
## Common Workflows
### Workflow 1: Load Model and Predict Growth
```python
from cobra.io import load_model
# Load model (textbook = fast tutorial; iJO1366 / iML1515 for genome-scale)
model = load_model("textbook")
# Run FBA
solution = model.optimize()
print(f"Growth rate: {solution.objective_value:.3f} /h")
# Show active pathways
print(solution.fluxes[solution.fluxes.abs() > 1e-6])
```
### Workflow 2: Gene Knockout Screen
```python
from cobra.io import load_model
from cobra.flux_analysis import single_gene_deletion
# Load model
model = load_model("textbook")
baseline = model.slim_optimize()
# Perform single gene deletions
results = single_gene_deletion(model)
# Find essential genes (growth < threshold)
essential_genes = results[results["growth"] < 0.01]
print(f"Found {len(essential_genes)} essential genes")
# Find genes with minimal impact
neutral_genes = results[results["growth"] > 0.9 * baseline]
```
### Workflow 3: Media Optimization
```python
from cobra.io import load_model
from cobra.medium import minimal_medium
# Load model
model = load_model("textbook")
# Calculate minimal medium for 50% of max growth
target_growth = model.slim_optimize() * 0.5
min_medium = minimal_medium(
model,
target_growth,
minimize_components=True
)
print(f"Minimal medium components: {len(min_medium)}")
print(min_medium)
```
### Workflow 4: Flux Uncertainty Analysis
```python
from cobra.io import load_model
from cobra.flux_analysis import flux_variability_analysis
from cobra.sampling import sample
# Load model
model = load_model("textbook")
# First check flux ranges at optimality
fva = flux_variability_analysis(model, fraction_of_optimum=1.0)
# For reactions with large ranges, sample to understand distribution
samples = sample(model, n=1000)
# Analyze specific reaction
reaction_id = "PFK"
import matplotlib.pyplot as plt
samples[reaction_id].hist(bins=50)
plt.xlabel(f"Flux through {reaction_id}")
plt.ylabel("Frequency")
plt.show()
```
### Workflow 5: Context Manager for Temporary Changes
Use context managers to make temporary modifications:
```python
# Model remains unchanged outside context
with model:
# Temporarily change objective
model.objective = "ATPM"
# Temporarily modify bounds
model.reactions.EX_glc__D_e.lower_bound = -5.0
# Temporarily knock out genes
model.genes.b0008.knock_out()
# Optimize with changes
solution = model.optimize()
print(f"Modified growth: {solution.objective_value}")
# All changes automatically reverted
solution = model.optimize()
print(f"Original growth: {solution.objective_value}")
```
## Key Concepts
### DictList Objects
Models use `DictList` objects for reactions, metabolites, and genes - behaving like both lists and dictionaries:
```python
# Access by index
first_reaction = model.reactions[0]
# Access by ID
pfk = model.reactions.get_by_id("PFK")
# Query methods
atp_reactions = model.reactions.query("atp")
```
### Flux Constraints
Reaction bounds define feasible flux ranges:
- **Irreversible**: `lower_bound = 0, upper_bound > 0`
- **Reversible**: `lower_bound < 0, upper_bound > 0`
- Set both bounds simultaneously with `.bounds` to avoid inconsistencies
### Gene-Reaction Rules (GPR)
Boolean logic linking genes to reactions:
```python
# AND logic (both required)
reaction.gene_reaction_rule = "gene1 and gene2"
# OR logic (either sufficient)
reaction.gene_reaction_rule = "gene1 or gene2"
# Complex logic
reaction.gene_reaction_rule = "(gene1 and gene2) or (gene3 and gene4)"
```
### Exchange Reactions
Special reactions representing metabolite import/export:
- Named with prefix `EX_` by convention
- Positive flux = secretion, negative flux = uptake
- Managed through `model.medium` dictionary
## Best Practices
1. **Use context managers** for temporary modifications to avoid state management issues
2. **Validate models** before analysis using `model.slim_optimize()` to ensure feasibility
3. **Check solution status** after optimization - `optimal` indicates successful solve
4. **Use loopless FVA** when thermodynamic feasibility matters
5. **Set fraction_of_optimum** appropriately in FVA to explore suboptimal space
6. **Parallelize** computationally expensive operations (sampling, double deletions) — start with small `n` and `processes=1` on genome-scale models
7. **Prefer SBML format** for model exchange and long-term storage
8. **Use slim_optimize()** when only objective value needed for performance
9. **Validate flux samples** to ensure numerical stability
10. **Confirm output paths** before writing CSV/PNG files from workflow examples
## Troubleshooting
**Infeasible solutions**: Check medium constraints, reaction bounds, and model consistency
**Slow optimization**: Try different solvers (GLPK, CPLEX, Gurobi) via `model.solver`
**Unbounded solutions**: Verify exchange reactions have appropriate upper bounds
**Import errors**: Ensure correct file format and valid SBML identifiers
## References
For detailed workflows and API patterns, refer to:
- `references/workflows.md` - Comprehensive step-by-step workflow examples
- `references/api_quick_reference.md` - Common function signatures and patterns
Official documentation: https://cobrapy.readthedocs.io/en/latest/
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