@synsci/cli-darwin-x64 1.1.76 → 1.1.78

package/bin/skills/cobrapy/references/workflows.md

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+# COBRApy Comprehensive Workflows
+
+This document provides detailed step-by-step workflows for common COBRApy tasks in metabolic modeling.
+
+## Workflow 1: Complete Knockout Study with Visualization
+
+This workflow demonstrates how to perform a comprehensive gene knockout study and visualize the results.
+
+```python
+import pandas as pd
+import matplotlib.pyplot as plt
+from cobra.io import load_model
+from cobra.flux_analysis import single_gene_deletion, double_gene_deletion
+
+# Step 1: Load model
+model = load_model("ecoli")
+print(f"Loaded model: {model.id}")
+print(f"Model contains {len(model.reactions)} reactions, {len(model.metabolites)} metabolites, {len(model.genes)} genes")
+
+# Step 2: Get baseline growth rate
+baseline = model.slim_optimize()
+print(f"Baseline growth rate: {baseline:.3f} /h")
+
+# Step 3: Perform single gene deletions
+print("Performing single gene deletions...")
+single_results = single_gene_deletion(model)
+
+# Step 4: Classify genes by impact
+essential_genes = single_results[single_results["growth"] < 0.01]
+severely_impaired = single_results[(single_results["growth"] >= 0.01) &
+                                   (single_results["growth"] < 0.5 * baseline)]
+moderately_impaired = single_results[(single_results["growth"] >= 0.5 * baseline) &
+                                     (single_results["growth"] < 0.9 * baseline)]
+neutral_genes = single_results[single_results["growth"] >= 0.9 * baseline]
+
+print(f"\nSingle Deletion Results:")
+print(f"  Essential genes: {len(essential_genes)}")
+print(f"  Severely impaired: {len(severely_impaired)}")
+print(f"  Moderately impaired: {len(moderately_impaired)}")
+print(f"  Neutral genes: {len(neutral_genes)}")
+
+# Step 5: Visualize distribution
+fig, ax = plt.subplots(figsize=(10, 6))
+single_results["growth"].hist(bins=50, ax=ax)
+ax.axvline(baseline, color='r', linestyle='--', label='Baseline')
+ax.set_xlabel("Growth rate (/h)")
+ax.set_ylabel("Number of genes")
+ax.set_title("Distribution of Growth Rates After Single Gene Deletions")
+ax.legend()
+plt.tight_layout()
+plt.savefig("single_deletion_distribution.png", dpi=300)
+
+# Step 6: Identify gene pairs for double deletions
+# Focus on non-essential genes to find synthetic lethals
+target_genes = single_results[single_results["growth"] >= 0.5 * baseline].index.tolist()
+target_genes = [list(gene)[0] for gene in target_genes[:50]]  # Limit for performance
+
+print(f"\nPerforming double deletions on {len(target_genes)} genes...")
+double_results = double_gene_deletion(
+    model,
+    gene_list1=target_genes,
+    processes=4
+)
+
+# Step 7: Find synthetic lethal pairs
+synthetic_lethals = double_results[
+    (double_results["growth"] < 0.01) &
+    (single_results.loc[double_results.index.get_level_values(0)]["growth"].values >= 0.5 * baseline) &
+    (single_results.loc[double_results.index.get_level_values(1)]["growth"].values >= 0.5 * baseline)
+]
+
+print(f"Found {len(synthetic_lethals)} synthetic lethal gene pairs")
+print("\nTop 10 synthetic lethal pairs:")
+print(synthetic_lethals.head(10))
+
+# Step 8: Export results
+single_results.to_csv("single_gene_deletions.csv")
+double_results.to_csv("double_gene_deletions.csv")
+synthetic_lethals.to_csv("synthetic_lethals.csv")
+```
+
+## Workflow 2: Media Design and Optimization
+
+This workflow shows how to systematically design growth media and find minimal media compositions.
+
+```python
+from cobra.io import load_model
+from cobra.medium import minimal_medium
+import pandas as pd
+
+# Step 1: Load model and check current medium
+model = load_model("ecoli")
+current_medium = model.medium
+print("Current medium composition:")
+for exchange, bound in current_medium.items():
+    metabolite_id = exchange.replace("EX_", "").replace("_e", "")
+    print(f"  {metabolite_id}: {bound:.2f} mmol/gDW/h")
+
+# Step 2: Get baseline growth
+baseline_growth = model.slim_optimize()
+print(f"\nBaseline growth rate: {baseline_growth:.3f} /h")
+
+# Step 3: Calculate minimal medium for different growth targets
+growth_targets = [0.25, 0.5, 0.75, 1.0]
+minimal_media = {}
+
+for fraction in growth_targets:
+    target_growth = baseline_growth * fraction
+    print(f"\nCalculating minimal medium for {fraction*100:.0f}% growth ({target_growth:.3f} /h)...")
+
+    min_medium = minimal_medium(
+        model,
+        target_growth,
+        minimize_components=True,
+        open_exchanges=True
+    )
+
+    minimal_media[fraction] = min_medium
+    print(f"  Required components: {len(min_medium)}")
+    print(f"  Components: {list(min_medium.index)}")
+
+# Step 4: Compare media compositions
+media_df = pd.DataFrame(minimal_media).fillna(0)
+media_df.to_csv("minimal_media_comparison.csv")
+
+# Step 5: Test aerobic vs anaerobic conditions
+print("\n--- Aerobic vs Anaerobic Comparison ---")
+
+# Aerobic
+model_aerobic = model.copy()
+aerobic_growth = model_aerobic.slim_optimize()
+aerobic_medium = minimal_medium(model_aerobic, aerobic_growth * 0.9, minimize_components=True)
+
+# Anaerobic
+model_anaerobic = model.copy()
+medium_anaerobic = model_anaerobic.medium
+medium_anaerobic["EX_o2_e"] = 0.0
+model_anaerobic.medium = medium_anaerobic
+anaerobic_growth = model_anaerobic.slim_optimize()
+anaerobic_medium = minimal_medium(model_anaerobic, anaerobic_growth * 0.9, minimize_components=True)
+
+print(f"Aerobic growth: {aerobic_growth:.3f} /h (requires {len(aerobic_medium)} components)")
+print(f"Anaerobic growth: {anaerobic_growth:.3f} /h (requires {len(anaerobic_medium)} components)")
+
+# Step 6: Identify unique requirements
+aerobic_only = set(aerobic_medium.index) - set(anaerobic_medium.index)
+anaerobic_only = set(anaerobic_medium.index) - set(aerobic_medium.index)
+shared = set(aerobic_medium.index) & set(anaerobic_medium.index)
+
+print(f"\nShared components: {len(shared)}")
+print(f"Aerobic-only: {aerobic_only}")
+print(f"Anaerobic-only: {anaerobic_only}")
+
+# Step 7: Test custom medium
+print("\n--- Testing Custom Medium ---")
+custom_medium = {
+    "EX_glc__D_e": 10.0,  # Glucose
+    "EX_o2_e": 20.0,       # Oxygen
+    "EX_nh4_e": 5.0,       # Ammonium
+    "EX_pi_e": 5.0,        # Phosphate
+    "EX_so4_e": 1.0,       # Sulfate
+}
+
+with model:
+    model.medium = custom_medium
+    custom_growth = model.optimize().objective_value
+    print(f"Growth on custom medium: {custom_growth:.3f} /h")
+
+    # Check which nutrients are limiting
+    for exchange in custom_medium:
+        with model:
+            # Double the uptake rate
+            medium_test = model.medium
+            medium_test[exchange] *= 2
+            model.medium = medium_test
+            test_growth = model.optimize().objective_value
+            improvement = (test_growth - custom_growth) / custom_growth * 100
+            if improvement > 1:
+                print(f"  {exchange}: +{improvement:.1f}% growth when doubled (LIMITING)")
+```
+
+## Workflow 3: Flux Space Exploration with Sampling
+
+This workflow demonstrates comprehensive flux space analysis using FVA and sampling.
+
+```python
+from cobra.io import load_model
+from cobra.flux_analysis import flux_variability_analysis
+from cobra.sampling import sample
+import pandas as pd
+import matplotlib.pyplot as plt
+import seaborn as sns
+
+# Step 1: Load model
+model = load_model("ecoli")
+baseline = model.slim_optimize()
+print(f"Baseline growth: {baseline:.3f} /h")
+
+# Step 2: Perform FVA at optimal growth
+print("\nPerforming FVA at optimal growth...")
+fva_optimal = flux_variability_analysis(model, fraction_of_optimum=1.0)
+
+# Step 3: Identify reactions with flexibility
+fva_optimal["range"] = fva_optimal["maximum"] - fva_optimal["minimum"]
+fva_optimal["relative_range"] = fva_optimal["range"] / (fva_optimal["maximum"].abs() + 1e-9)
+
+flexible_reactions = fva_optimal[fva_optimal["range"] > 1.0].sort_values("range", ascending=False)
+print(f"\nFound {len(flexible_reactions)} reactions with >1.0 mmol/gDW/h flexibility")
+print("\nTop 10 most flexible reactions:")
+print(flexible_reactions.head(10)[["minimum", "maximum", "range"]])
+
+# Step 4: Perform FVA at suboptimal growth (90%)
+print("\nPerforming FVA at 90% optimal growth...")
+fva_suboptimal = flux_variability_analysis(model, fraction_of_optimum=0.9)
+fva_suboptimal["range"] = fva_suboptimal["maximum"] - fva_suboptimal["minimum"]
+
+# Step 5: Compare flexibility at different optimality levels
+comparison = pd.DataFrame({
+    "range_100": fva_optimal["range"],
+    "range_90": fva_suboptimal["range"]
+})
+comparison["range_increase"] = comparison["range_90"] - comparison["range_100"]
+
+print("\nReactions with largest increase in flexibility at suboptimality:")
+print(comparison.sort_values("range_increase", ascending=False).head(10))
+
+# Step 6: Perform flux sampling
+print("\nPerforming flux sampling (1000 samples)...")
+samples = sample(model, n=1000, method="optgp", processes=4)
+
+# Step 7: Analyze sampling results for key reactions
+key_reactions = ["PFK", "FBA", "TPI", "GAPD", "PGK", "PGM", "ENO", "PYK"]
+available_key_reactions = [r for r in key_reactions if r in samples.columns]
+
+if available_key_reactions:
+    fig, axes = plt.subplots(2, 4, figsize=(16, 8))
+    axes = axes.flatten()
+
+    for idx, reaction_id in enumerate(available_key_reactions[:8]):
+        ax = axes[idx]
+        samples[reaction_id].hist(bins=30, ax=ax, alpha=0.7)
+
+        # Overlay FVA bounds
+        fva_min = fva_optimal.loc[reaction_id, "minimum"]
+        fva_max = fva_optimal.loc[reaction_id, "maximum"]
+        ax.axvline(fva_min, color='r', linestyle='--', label='FVA min')
+        ax.axvline(fva_max, color='r', linestyle='--', label='FVA max')
+
+        ax.set_xlabel("Flux (mmol/gDW/h)")
+        ax.set_ylabel("Frequency")
+        ax.set_title(reaction_id)
+        if idx == 0:
+            ax.legend()
+
+    plt.tight_layout()
+    plt.savefig("flux_distributions.png", dpi=300)
+
+# Step 8: Calculate correlation between reactions
+print("\nCalculating flux correlations...")
+correlation_matrix = samples[available_key_reactions].corr()
+
+fig, ax = plt.subplots(figsize=(10, 8))
+sns.heatmap(correlation_matrix, annot=True, fmt=".2f", cmap="coolwarm",
+            center=0, ax=ax, square=True)
+ax.set_title("Flux Correlations Between Key Glycolysis Reactions")
+plt.tight_layout()
+plt.savefig("flux_correlations.png", dpi=300)
+
+# Step 9: Identify reaction modules (highly correlated groups)
+print("\nHighly correlated reaction pairs (|r| > 0.9):")
+for i in range(len(correlation_matrix)):
+    for j in range(i+1, len(correlation_matrix)):
+        corr = correlation_matrix.iloc[i, j]
+        if abs(corr) > 0.9:
+            print(f"  {correlation_matrix.index[i]} <-> {correlation_matrix.columns[j]}: {corr:.3f}")
+
+# Step 10: Export all results
+fva_optimal.to_csv("fva_optimal.csv")
+fva_suboptimal.to_csv("fva_suboptimal.csv")
+samples.to_csv("flux_samples.csv")
+correlation_matrix.to_csv("flux_correlations.csv")
+```
+
+## Workflow 4: Production Strain Design
+
+This workflow demonstrates how to design a production strain for a target metabolite.
+
+```python
+from cobra.io import load_model
+from cobra.flux_analysis import (
+    production_envelope,
+    flux_variability_analysis,
+    single_gene_deletion
+)
+import pandas as pd
+import matplotlib.pyplot as plt
+
+# Step 1: Define production target
+TARGET_METABOLITE = "EX_ac_e"  # Acetate production
+CARBON_SOURCE = "EX_glc__D_e"  # Glucose uptake
+
+# Step 2: Load model
+model = load_model("ecoli")
+print(f"Designing strain for {TARGET_METABOLITE} production")
+
+# Step 3: Calculate baseline production envelope
+print("\nCalculating production envelope...")
+envelope = production_envelope(
+    model,
+    reactions=[CARBON_SOURCE, TARGET_METABOLITE],
+    carbon_sources=CARBON_SOURCE
+)
+
+# Visualize production envelope
+fig, ax = plt.subplots(figsize=(10, 6))
+ax.plot(envelope[CARBON_SOURCE], envelope["mass_yield_maximum"], 'b-', label='Max yield')
+ax.plot(envelope[CARBON_SOURCE], envelope["mass_yield_minimum"], 'r-', label='Min yield')
+ax.set_xlabel(f"Glucose uptake (mmol/gDW/h)")
+ax.set_ylabel(f"Acetate yield")
+ax.set_title("Wild-type Production Envelope")
+ax.legend()
+ax.grid(True, alpha=0.3)
+plt.tight_layout()
+plt.savefig("production_envelope_wildtype.png", dpi=300)
+
+# Step 4: Maximize production while maintaining growth
+print("\nOptimizing for production...")
+
+# Set minimum growth constraint
+MIN_GROWTH = 0.1  # Maintain at least 10% of max growth
+
+with model:
+    # Change objective to product formation
+    model.objective = TARGET_METABOLITE
+    model.objective_direction = "max"
+
+    # Add growth constraint
+    growth_reaction = model.reactions.get_by_id(model.objective.name) if hasattr(model.objective, 'name') else list(model.objective.variables.keys())[0].name
+    max_growth = model.slim_optimize()
+
+model.reactions.BIOMASS_Ecoli_core_w_GAM.lower_bound = MIN_GROWTH
+
+with model:
+    model.objective = TARGET_METABOLITE
+    model.objective_direction = "max"
+    production_solution = model.optimize()
+
+    max_production = production_solution.objective_value
+    print(f"Maximum production: {max_production:.3f} mmol/gDW/h")
+    print(f"Growth rate: {production_solution.fluxes['BIOMASS_Ecoli_core_w_GAM']:.3f} /h")
+
+# Step 5: Identify beneficial gene knockouts
+print("\nScreening for beneficial knockouts...")
+
+# Reset model
+model.reactions.BIOMASS_Ecoli_core_w_GAM.lower_bound = MIN_GROWTH
+model.objective = TARGET_METABOLITE
+model.objective_direction = "max"
+
+knockout_results = []
+for gene in model.genes:
+    with model:
+        gene.knock_out()
+        try:
+            solution = model.optimize()
+            if solution.status == "optimal":
+                production = solution.objective_value
+                growth = solution.fluxes["BIOMASS_Ecoli_core_w_GAM"]
+
+                if production > max_production * 1.05:  # >5% improvement
+                    knockout_results.append({
+                        "gene": gene.id,
+                        "production": production,
+                        "growth": growth,
+                        "improvement": (production / max_production - 1) * 100
+                    })
+        except:
+            continue
+
+knockout_df = pd.DataFrame(knockout_results)
+if len(knockout_df) > 0:
+    knockout_df = knockout_df.sort_values("improvement", ascending=False)
+    print(f"\nFound {len(knockout_df)} beneficial knockouts:")
+    print(knockout_df.head(10))
+    knockout_df.to_csv("beneficial_knockouts.csv", index=False)
+else:
+    print("No beneficial single knockouts found")
+
+# Step 6: Test combination of best knockouts
+if len(knockout_df) > 0:
+    print("\nTesting knockout combinations...")
+    top_genes = knockout_df.head(3)["gene"].tolist()
+
+    with model:
+        for gene_id in top_genes:
+            model.genes.get_by_id(gene_id).knock_out()
+
+        solution = model.optimize()
+        if solution.status == "optimal":
+            combined_production = solution.objective_value
+            combined_growth = solution.fluxes["BIOMASS_Ecoli_core_w_GAM"]
+            combined_improvement = (combined_production / max_production - 1) * 100
+
+            print(f"\nCombined knockout results:")
+            print(f"  Genes: {', '.join(top_genes)}")
+            print(f"  Production: {combined_production:.3f} mmol/gDW/h")
+            print(f"  Growth: {combined_growth:.3f} /h")
+            print(f"  Improvement: {combined_improvement:.1f}%")
+
+# Step 7: Analyze flux distribution in production strain
+if len(knockout_df) > 0:
+    best_gene = knockout_df.iloc[0]["gene"]
+
+    with model:
+        model.genes.get_by_id(best_gene).knock_out()
+        solution = model.optimize()
+
+        # Get active pathways
+        active_fluxes = solution.fluxes[solution.fluxes.abs() > 0.1]
+        active_fluxes.to_csv(f"production_strain_fluxes_{best_gene}_knockout.csv")
+
+        print(f"\nActive reactions in production strain: {len(active_fluxes)}")
+```
+
+## Workflow 5: Model Validation and Debugging
+
+This workflow shows systematic approaches to validate and debug metabolic models.
+
+```python
+from cobra.io import load_model, read_sbml_model
+from cobra.flux_analysis import flux_variability_analysis
+import pandas as pd
+
+# Step 1: Load model
+model = load_model("ecoli")  # Or read_sbml_model("your_model.xml")
+print(f"Model: {model.id}")
+print(f"Reactions: {len(model.reactions)}")
+print(f"Metabolites: {len(model.metabolites)}")
+print(f"Genes: {len(model.genes)}")
+
+# Step 2: Check model feasibility
+print("\n--- Feasibility Check ---")
+try:
+    objective_value = model.slim_optimize()
+    print(f"Model is feasible (objective: {objective_value:.3f})")
+except:
+    print("Model is INFEASIBLE")
+    print("Troubleshooting steps:")
+
+    # Check for blocked reactions
+    from cobra.flux_analysis import find_blocked_reactions
+    blocked = find_blocked_reactions(model)
+    print(f"  Blocked reactions: {len(blocked)}")
+    if len(blocked) > 0:
+        print(f"  First 10 blocked: {list(blocked)[:10]}")
+
+    # Check medium
+    print(f"\n  Current medium: {model.medium}")
+
+    # Try opening all exchanges
+    for reaction in model.exchanges:
+        reaction.lower_bound = -1000
+
+    try:
+        objective_value = model.slim_optimize()
+        print(f"\n  Model feasible with open exchanges (objective: {objective_value:.3f})")
+        print("  Issue: Medium constraints too restrictive")
+    except:
+        print("\n  Model still infeasible with open exchanges")
+        print("  Issue: Structural problem (missing reactions, mass imbalance, etc.)")
+
+# Step 3: Check mass and charge balance
+print("\n--- Mass and Charge Balance Check ---")
+unbalanced_reactions = []
+for reaction in model.reactions:
+    try:
+        balance = reaction.check_mass_balance()
+        if balance:
+            unbalanced_reactions.append({
+                "reaction": reaction.id,
+                "imbalance": balance
+            })
+    except:
+        pass
+
+if unbalanced_reactions:
+    print(f"Found {len(unbalanced_reactions)} unbalanced reactions:")
+    for item in unbalanced_reactions[:10]:
+        print(f"  {item['reaction']}: {item['imbalance']}")
+else:
+    print("All reactions are mass balanced")
+
+# Step 4: Identify dead-end metabolites
+print("\n--- Dead-end Metabolite Check ---")
+dead_end_metabolites = []
+for metabolite in model.metabolites:
+    producing_reactions = [r for r in metabolite.reactions
+                          if r.metabolites[metabolite] > 0]
+    consuming_reactions = [r for r in metabolite.reactions
+                          if r.metabolites[metabolite] < 0]
+
+    if len(producing_reactions) == 0 or len(consuming_reactions) == 0:
+        dead_end_metabolites.append({
+            "metabolite": metabolite.id,
+            "producers": len(producing_reactions),
+            "consumers": len(consuming_reactions)
+        })
+
+if dead_end_metabolites:
+    print(f"Found {len(dead_end_metabolites)} dead-end metabolites:")
+    for item in dead_end_metabolites[:10]:
+        print(f"  {item['metabolite']}: {item['producers']} producers, {item['consumers']} consumers")
+else:
+    print("No dead-end metabolites found")
+
+# Step 5: Check for duplicate reactions
+print("\n--- Duplicate Reaction Check ---")
+reaction_equations = {}
+duplicates = []
+
+for reaction in model.reactions:
+    equation = reaction.build_reaction_string()
+    if equation in reaction_equations:
+        duplicates.append({
+            "reaction1": reaction_equations[equation],
+            "reaction2": reaction.id,
+            "equation": equation
+        })
+    else:
+        reaction_equations[equation] = reaction.id
+
+if duplicates:
+    print(f"Found {len(duplicates)} duplicate reaction pairs:")
+    for item in duplicates[:10]:
+        print(f"  {item['reaction1']} == {item['reaction2']}")
+else:
+    print("No duplicate reactions found")
+
+# Step 6: Identify orphan genes
+print("\n--- Orphan Gene Check ---")
+orphan_genes = [gene for gene in model.genes if len(gene.reactions) == 0]
+
+if orphan_genes:
+    print(f"Found {len(orphan_genes)} orphan genes (not associated with reactions):")
+    print(f"  First 10: {[g.id for g in orphan_genes[:10]]}")
+else:
+    print("No orphan genes found")
+
+# Step 7: Check for thermodynamically infeasible loops
+print("\n--- Thermodynamic Loop Check ---")
+fva_loopless = flux_variability_analysis(model, loopless=True)
+fva_standard = flux_variability_analysis(model)
+
+loop_reactions = []
+for reaction_id in fva_standard.index:
+    standard_range = fva_standard.loc[reaction_id, "maximum"] - fva_standard.loc[reaction_id, "minimum"]
+    loopless_range = fva_loopless.loc[reaction_id, "maximum"] - fva_loopless.loc[reaction_id, "minimum"]
+
+    if standard_range > loopless_range + 0.1:
+        loop_reactions.append({
+            "reaction": reaction_id,
+            "standard_range": standard_range,
+            "loopless_range": loopless_range
+        })
+
+if loop_reactions:
+    print(f"Found {len(loop_reactions)} reactions potentially involved in loops:")
+    loop_df = pd.DataFrame(loop_reactions).sort_values("standard_range", ascending=False)
+    print(loop_df.head(10))
+else:
+    print("No thermodynamically infeasible loops detected")
+
+# Step 8: Generate validation report
+print("\n--- Generating Validation Report ---")
+validation_report = {
+    "model_id": model.id,
+    "feasible": objective_value if 'objective_value' in locals() else None,
+    "n_reactions": len(model.reactions),
+    "n_metabolites": len(model.metabolites),
+    "n_genes": len(model.genes),
+    "n_unbalanced": len(unbalanced_reactions),
+    "n_dead_ends": len(dead_end_metabolites),
+    "n_duplicates": len(duplicates),
+    "n_orphan_genes": len(orphan_genes),
+    "n_loop_reactions": len(loop_reactions)
+}
+
+validation_df = pd.DataFrame([validation_report])
+validation_df.to_csv("model_validation_report.csv", index=False)
+print("Validation report saved to model_validation_report.csv")
+```
+
+These workflows provide comprehensive templates for common COBRApy tasks. Adapt them as needed for specific research questions and models.