End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA analysis, and gene essentiality prediction. Use when building metabolic models or predicting metabolic phenotypes from genomic data.
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End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA analysis, and gene essentiality prediction. Use when building metabolic models or predicting metabolic phenotypes from genomic data.
[{"after_reconstruction":"Reactions 1000-2500, growth >0.01 on target media"},{"after_curation":"Memote score >50%, <5% orphan reactions"},{"after_fba":"Realistic growth rate, major pathways active"},{"after_essentiality":"Core essential genes match literature >70%"}]
Metabolic Modeling Pipeline
Complete workflow for genome-scale metabolic modeling: from protein sequences to flux predictions and phenotype analysis.
Workflow Overview
Protein FASTA (genome annotation)
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[1. Reconstruction] --> CarveMe / gapseq / ModelSEED
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[2. Model Curation] --> memote QC, gap-filling
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| <---- Iterative refinement loop
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[3. FBA Analysis] --> Growth prediction, flux distribution
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+-----------------------+
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[4a. Gene Essentiality] [4b. Context-Specific]
Single/double KO Tissue-specific models
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Essential Gene List Condition-Specific Fluxes
# Basic reconstruction from protein sequences
carve genome.faa -o model_draft.xml
# With gram type specification (improves biomass composition)
carve genome.faa -o model_draft.xml --gram-neg
# Gap-fill for specific media
carve genome.faa -o model_draft.xml --gram-neg --gapfill M9
# Run memote QC
memote run --filename model_draft_report.html model_draft.xml
# Generate snapshot for comparison
memote report snapshot --filename model_snapshot.json model_draft.xml
import json
withopen('model_snapshot.json') as f:
report = json.load(f)
# Key metrics to check
metrics = report['tests']['basic']
print('=== Model QC Metrics ===')
print(f"Reactions with genes: {metrics.get('test_gene_reaction_rule_presence', {}).get('metric', 'N/A')}")
print(f"Metabolites in reactions: {metrics.get('test_metabolites_not_produced', {}).get('metric', 'N/A')}")
print(f"Stoichiometry balance: {metrics.get('test_stoichiometric_consistency', {}).get('result', 'N/A')}")
# Target: memote score >50% for usable model# Score >70% indicates well-curated model
total_score = report.get('score', {}).get('total_score', 0)
print(f'Total memote score: {total_score:.1%}')
Step 3: Model Curation (Iterative)
import cobra
from cobra.flux_analysis import gapfill
model = cobra.io.read_sbml_model('model_draft.xml')
# Check for common issuesdefdiagnose_model(model):
issues = []
# Dead-end metabolites (produced but not consumed, or vice versa)for met in model.metabolites:
producing = [r for r in met.reactions if met in r.products]
consuming = [r for r in met.reactions if met in r.reactants]
iflen(producing) > 0andlen(consuming) == 0:
issues.append(f'Dead-end (not consumed): {met.id}')
eliflen(producing) == 0andlen(consuming) > 0:
issues.append(f'Dead-end (not produced): {met.id}')
# Blocked reactions
fva = cobra.flux_analysis.flux_variability_analysis(model)
blocked = fva[(fva['minimum'] == 0) & (fva['maximum'] == 0)]
iflen(blocked) > 0:
issues.append(f'Blocked reactions: {len(blocked)}')
return issues
issues = diagnose_model(model)
print(f'Found {len(issues)} issues')
for issue in issues[:10]:
print(f' {issue}')
# Gap-filling for growth on specific mediafrom cobra.medium import minimal_medium
# Load universal reaction database for gap-filling
universal = cobra.io.read_sbml_model('universal_model.xml')
# Define target medium (e.g., glucose minimal)
target_medium = {
'EX_glc__D_e': 10, # Glucose uptake'EX_o2_e': 20, # Oxygen'EX_nh4_e': 100, # Ammonium'EX_pi_e': 100, # Phosphate'EX_so4_e': 100, # Sulfate
}
# Apply mediumfor rxn_id in model.exchanges:
rxn = model.reactions.get_by_id(rxn_id)
if rxn_id in target_medium:
rxn.lower_bound = -target_medium[rxn_id]
else:
rxn.lower_bound = 0# Block other uptakes# Gap-fill to enable growth# Gap-filling adds minimal reactions from universal model to enable growth
gapfill_solution = gapfill(model, universal, demand_reactions=False)
print(f'Gap-fill added {len(gapfill_solution[0])} reactions')
for rxn in gapfill_solution[0]:
model.add_reactions([rxn])
print(f' Added: {rxn.id} - {rxn.name}')
# Verify growth
solution = model.optimize()
print(f'Growth after gap-fill: {solution.objective_value:.4f} h^-1')
Step 4: Flux Balance Analysis
import cobra
import pandas as pd
import matplotlib.pyplot as plt
model = cobra.io.read_sbml_model('model_curated.xml')
# Basic FBA
solution = model.optimize()
print(f'Objective (growth): {solution.objective_value:.4f} h^-1')
print(f'Status: {solution.status}')
# Get active fluxes
fluxes = solution.fluxes
active_fluxes = fluxes[abs(fluxes) > 1e-6]
print(f'Active reactions: {len(active_fluxes)} / {len(model.reactions)}')
# Key exchange fluxes (uptake/secretion)
exchange_fluxes = fluxes[[r.idfor r in model.exchanges]]
significant_exchanges = exchange_fluxes[abs(exchange_fluxes) > 0.1]
print('\nSignificant exchanges:')
print(significant_exchanges.sort_values())
from cobra.flux_analysis import single_gene_deletion, double_gene_deletion
# Single gene knockouts
single_ko = single_gene_deletion(model)
single_ko['growth_ratio'] = single_ko['growth'] / solution.objective_value
# Essential genes: knockout abolishes growth (<10% of WT)# Threshold 0.1 is standard for essentiality
essential = single_ko[single_ko['growth_ratio'] < 0.1]
print(f'Essential genes: {len(essential)} / {len(model.genes)}')
# Export essential genes
essential_list = [list(g)[0].idfor g in essential.index]
withopen('essential_genes.txt', 'w') as f:
f.write('\n'.join(essential_list))
# Compare to experimental data (if available)# Typically expect >70% overlap with experimental essentiality screens
# Double gene knockouts (synthetic lethality)# WARNING: Computationally intensive for large models# Focus on non-essential genes only
non_essential = [g.idfor g in model.genes if g.idnotin essential_list]
# Run pairwise deletions
double_ko = double_gene_deletion(model, gene_list=non_essential[:100]) # Subset for speed# Find synthetic lethal pairs# Synthetic lethality: neither single KO is lethal, but double KO is
synthetic_lethal = double_ko[double_ko['growth'] < 0.01]
print(f'Synthetic lethal pairs: {len(synthetic_lethal)}')
Step 5b: Context-Specific Models
# Build tissue-specific model using expression datadefbuild_context_model(model, expression_data, threshold_percentile=25):
'''Build context-specific model by removing lowly-expressed reactions.
threshold_percentile: reactions below this expression percentile are candidates for removal
'''import numpy as np
context_model = model.copy()
threshold = np.percentile(list(expression_data.values()), threshold_percentile)
reactions_to_remove = []
for rxn in context_model.reactions:
if rxn.gene_reaction_rule:
genes_in_rxn = [g.idfor g in rxn.genes]
# Get expression for genes in reaction
expr_values = [expression_data.get(g, 0) for g in genes_in_rxn]
# If all genes below threshold, candidate for removalifall(e < threshold for e in expr_values):
# Check if removal breaks growthwith context_model:
rxn.knock_out()
sol = context_model.optimize()
if sol.objective_value > 0.01:
reactions_to_remove.append(rxn.id)
for rxn_id in reactions_to_remove:
context_model.reactions.get_by_id(rxn_id).remove_from_model()
return context_model
# Example: liver-specific model
liver_expression = {'gene1': 100, 'gene2': 5, 'gene3': 50} # TPM values
liver_model = build_context_model(model, liver_expression)
print(f'Liver model: {len(liver_model.reactions)} reactions')
Visualization with Escher
import escher
# Load model and solution
model = cobra.io.read_sbml_model('model_curated.xml')
solution = model.optimize()
# Create Escher map
builder = escher.Builder(
map_name='e_coli_core.Core metabolism',
model=model,
reaction_data=solution.fluxes.to_dict()
)
builder.save_html('flux_map.html')
