bio-systems-biology-metabolic-reconstruction

What problem does it solve?

This skill automates building genome-scale metabolic models from genome sequences, removing manual mapping of protein sequences to metabolic reactions and ad hoc gap-filling so researchers can obtain draft SBML/JSON models quickly.

Core Features & Use Cases

• Automated reconstruction: Use CarveMe or gapseq to convert protein FASTA or genomic inputs into draft metabolic models.
• Gap-filling and media control: Apply gap-filling for defined media (for example M9 or LB) to produce models capable of growth simulations.
• Batch and community workflows: Reconstruct models for many genomes in batch and merge models into community models for microbiome FBA.
• Model inspection and quality checks: Load outputs with COBRApy to report reactions, metabolites, genes, orphan reactions, and to test growth and basic quality metrics.

Quick Start

Reconstruct a metabolic model from a protein FASTA file genome.faa and save the draft SBML as model.xml using CarveMe.