GEMtractor

GEMtractor extracts subnetworks from SBML-encoded genome-scale metabolic models (GEMs) to enable focused analysis and comparison of metabolic pathways and enzymatic functions.

Key Features:

• Model Trimming and Extraction: Trims genome-scale metabolic models encoded in SBML to isolate subnetworks centered on specified reactions or enzymes.
• Reaction-Centric and Enzyme-Centric Views: Generates reaction-centric and enzyme-centric representations of GEMs for targeted analysis of pathways and enzymatic functions.
• SBML Parsing: Parses SBML-encoded GEMs to identify species, reactions, and enzyme annotations.
• Multipartite Graph Topological Analysis: Performs topological analysis on multipartite graphs representing species, reactions, and enzymes within models.
• User-Defined Extraction Criteria: Applies user-defined criteria to select and extract desired subnetworks from GEMs.

Scientific Applications:

• Focused Pathway and Enzyme Studies: Enables targeted analysis of particular metabolic pathways or enzyme functions by extracting relevant subnetworks.
• Comparative Analysis of Metabolic Models: Simplifies comparison of metabolic models by reducing them to relevant subcomponents for direct comparison.
• Computational Efficiency for Network Analysis: Enhances computational efficiency by enabling analyses on smaller, more manageable network segments.

Methodology:

Parses SBML-encoded GEMs, constructs multipartite graphs of species, reactions, and enzymes, applies user-defined criteria, and performs topological analysis to extract trimmed reaction- or enzyme-centric subnetworks.