bio-systems-biology-metabolic-reconstruction

name	bio-systems-biology-metabolic-reconstruction
description	Build genome-scale metabolic models (GEMs) from genome sequences using CarveMe and gapseq for automated reconstruction. Use when: user wants to build a metabolic model from a genome, create a GEM for a new organism, reconstruct metabolism from FASTA/GenBank, or generate a draft SBML model. Triggers: build metabolic model, genome-scale model, CarveMe, gapseq, metabolic reconstruction, GEM, draft model, SBML generation, organism-specific model, de novo metabolic model, reconstruct metabolism.
tool_type	cli
primary_tool	CarveMe
upstream	{"repo":"https://github.com/GPTomics/bioSkills","license":"MIT","original_author":"GPTomics"}

Version Compatibility

Reference examples tested with: COBRApy 0.29+, NCBI BLAST+ 2.15+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Metabolic Reconstruction

"Build a metabolic model for my organism from its genome" → Generate a genome-scale metabolic model by mapping protein sequences to a universal reaction database, then gap-filling to ensure growth capability on specified media.

• CLI: carve (CarveMe) for automated reconstruction from protein FASTA
• CLI: gapseq find + gapseq draft + gapseq fill for pathway-based reconstruction

CarveMe (Recommended)

# Install CarveMe
pip install carveme

# Basic reconstruction from protein FASTA
carve genome.faa -o model.xml

# Specify output format
carve genome.faa -o model.xml --format sbml
carve genome.faa -o model.json --format json

# Gap-fill for specific media
carve genome.faa -o model.xml --gapfill M9

# Available media: M9, LB, M9[glc], M9[glyc], etc.

CarveMe Options

# Use diamond instead of blastp (faster)
carve genome.faa -o model.xml --diamond

# Specify organism type
carve genome.faa -o model.xml --grampos  # Gram-positive
carve genome.faa -o model.xml --gramneg  # Gram-negative (default)

# Initialize from template model
carve genome.faa -o model.xml --init M9

# Verbose output for debugging
carve genome.faa -o model.xml -v

gapseq (Alternative)

# Install gapseq
git clone https://github.com/jotech/gapseq
cd gapseq
./gapseq check  # Check dependencies

# Full reconstruction workflow
./gapseq find -p all genome.fasta  # Find metabolic pathways
./gapseq find -t all genome.fasta  # Find transporters
./gapseq draft -r genome-all-Reactions.tbl \
               -t genome-Transporters.tbl \
               -p genome-all-Pathways.tbl \
               -c genome.fasta
./gapseq fill -m genome-draft.RDS -c genome.fasta -n M9

Python API for CarveMe

import subprocess

def reconstruct_model(fasta_path, output_path, media='M9', grampos=False):
    '''Run CarveMe reconstruction

    Args:
        fasta_path: Path to protein FASTA file
        output_path: Output model file path (.xml or .json)
        media: Gap-filling media (M9, LB, etc.)
        grampos: True for Gram-positive organisms

    Model size expectations:
    - Bacteria: 1000-2500 reactions typical
    - Fungi: 1500-3000 reactions
    - Archaea: 800-1500 reactions
    '''
    cmd = ['carve', fasta_path, '-o', output_path, '--gapfill', media]

    if grampos:
        cmd.append('--grampos')

    subprocess.run(cmd, check=True)
    return output_path

Load and Inspect Draft Model

import cobra

model = cobra.io.read_sbml_model('model.xml')

print(f'Reactions: {len(model.reactions)}')
print(f'Metabolites: {len(model.metabolites)}')
print(f'Genes: {len(model.genes)}')

# Check if model can grow
solution = model.optimize()
print(f'Growth rate: {solution.objective_value:.4f}')

# List exchange reactions (available nutrients)
for rxn in model.exchanges[:10]:
    print(f'{rxn.id}: {rxn.reaction}')

Quality Metrics

def assess_model_quality(model):
    '''Basic quality assessment for draft model

    Returns metrics to evaluate reconstruction quality.
    '''
    metrics = {
        'reactions': len(model.reactions),
        'metabolites': len(model.metabolites),
        'genes': len(model.genes),
        'gene_reaction_ratio': len(model.reactions) / max(1, len(model.genes))
    }

    # Count reaction types
    metrics['exchanges'] = len(model.exchanges)
    metrics['transport'] = len([r for r in model.reactions if 'transport' in r.name.lower()])

    # Test growth
    sol = model.optimize()
    metrics['can_grow'] = sol.status == 'optimal' and sol.objective_value > 0.001

    # Gene-reaction rules
    metrics['orphan_reactions'] = len([r for r in model.reactions if not r.genes])

    return metrics

Multiple Genome Reconstruction

import os
from pathlib import Path

def batch_reconstruction(fasta_dir, output_dir, media='M9'):
    '''Reconstruct models for multiple genomes

    Use for comparative genomics or community modeling.
    '''
    os.makedirs(output_dir, exist_ok=True)

    for fasta in Path(fasta_dir).glob('*.faa'):
        output = Path(output_dir) / f'{fasta.stem}.xml'
        reconstruct_model(str(fasta), str(output), media=media)
        print(f'Completed: {fasta.name}')

Community Model Construction

def merge_models(model_paths, community_name='community'):
    '''Create community model from individual organisms

    For microbiome FBA, need to create a shared compartment
    for metabolite exchange between organisms.
    '''
    import cobra

    models = [cobra.io.read_sbml_model(p) for p in model_paths]

    # Add species prefix to all components
    for i, model in enumerate(models):
        species_id = f'sp{i+1}'
        for rxn in model.reactions:
            rxn.id = f'{species_id}_{rxn.id}'
        for met in model.metabolites:
            met.id = f'{species_id}_{met.id}'
        for gene in model.genes:
            gene.id = f'{species_id}_{gene.id}'

    # Merge into community model
    community = models[0].copy()
    for model in models[1:]:
        community.merge(model)

    return community

Related Skills

• systems-biology/model-curation - Validate and curate draft models
• systems-biology/flux-balance-analysis - Analyze reconstructed models
• database-access/entrez-fetch - Download genome sequences