bio-systems-biology-model-curation

What problem does it solve?

Validate, score, and improve genome-scale metabolic models to identify SBML compliance issues, memote failures, dead-end metabolites, unbalanced reactions, and incomplete annotations so models produce biologically meaningful predictions.

Core Features & Use Cases

• Memote scoring and reports: Run memote snapshot and parse test failures to prioritize fixes for publication-quality models.
• Automated gap-filling: Suggest and apply reactions from a universal model to restore growth or pathway connectivity.
• Model debugging: Detect dead-end metabolites, unbalanced reactions, and orphan reactions and standardize GPR rules and annotations.
• Use Case: Run a memote assessment on a draft SBML model, perform gap-filling with a universal model, fix stoichiometric imbalances, and export a curated SBML for downstream FBA.

Quick Start

Ask the agent to "Run memote on my model.xml, list failing tests, find dead-end metabolites, attempt gap-filling using a provided universal model, and save a curated model as curated_model.xml".