ModelExplorer

ModelExplorer visualizes and facilitates correction of inconsistencies in genome-scale metabolic reconstructions to enable accurate system-level metabolic analyses such as Flux Balance Analysis (FBA).

Key Features:

• Consistency Checking Modes: Multiple modes for identifying topological and stoichiometric inconsistencies and locating parts of the model that cannot carry flux.
• Blocked Reaction and Metabolite Detection: Identification of reactions and species that are blocked or unable to carry flux under any condition.
• Graph-based Metabolic Network Visualization: Automatic visualization of metabolic networks as graphs with explicit separation and delineation of cellular compartments.
• Automatic Neighbor and Pathway Identification: Automatic pinpointing of neighbor metabolites and production pathways for any specified species or reaction.
• Focused Subnetwork Isolation: Isolation and focused analysis of inconsistent subnetworks to narrow down problematic reactions and species.
• Editable Model Elements: Capability to edit, add, or delete reactions, metabolites, and other model components to correct identified issues.
• Consistency Checking Algorithms and Tracking Tools: Integration of consistency-checking algorithms with tracking tools and real-time visualization updates to support systematic model correction.

Scientific Applications:

• Flux Balance Analysis preparation: Refinement and validation of genome-scale metabolic models for accurate FBA and related constraint-based analyses.
• Model curation: Manual curation and correction of topological and stoichiometric errors in metabolic reconstructions.
• Blocked-pathway analysis: Detection and resolution of blocked reactions and metabolites to restore network connectivity and metabolic functionality.
• Preparation for downstream analyses: Ensuring model consistency prior to downstream computational studies that depend on complete and flux-carrying network regions.

Methodology:

Visualization of metabolic networks as compartmentalized graphs; application of multiple consistency-checking modes and algorithms; automatic neighbor and production-pathway identification; isolation of inconsistent subnetworks; editable model element operations; tracking tools with real-time visualization updates.