DORMAN

DORMAN provides a centralized repository of reconstructed genome-scale metabolic networks in Systems Biology Markup Language (SBML) and enables analysis, visualization, and comparison of these models to support studies of cellular metabolism.

Key Features:

• Centralized Repository: Stores reconstructed metabolic networks in SBML format sourced from published literature.
• Visualization and Editing: Renders complete network structures and supports editing and export of models.
• Hierarchical Navigation: Enables navigation of interconnected entities within metabolic networks.
• Query Interface: Supports topological queries on stored models.
• Model Comparison: Compares different metabolic models using approximate string matching to accommodate varying nomenclatures.
• Compatibility for Constraint-Based Analyses: SBML storage ensures interoperability with constraint-based analysis tools.
• Organism-Specific Models: Houses organism-specific metabolic models to support comparative and organism-focused studies.

Scientific Applications:

• Network Topology Analysis: Enables study of metabolic network topology through topological queries and visualization.
• Model Comparison: Facilitates identification of conserved pathways and unique metabolic features across organisms via approximate string matching comparisons.
• Data Integration: Supports integration of new data into existing reconstructed networks for model refinement.
• Constraint-Based Modeling: Enables use of stored SBML models in constraint-based analyses of metabolic function and phenotype.

Methodology:

Models are stored in SBML; features include rendering of network structures, hierarchical navigation, topological query execution, model editing/export, and model comparison using approximate string matching.