bio-systems-biology-metabolic-reconstruction

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