SAMMI

SAMMI visualizes metabolic networks to facilitate interpretation of KEGG-annotated pathways and constraint-based genome-scale model simulation results.

Key Features:

• Automated network partitioning and navigation: Performs automated partitioning and navigation to manage and explore large-scale metabolic networks.
• Manual map editing: Provides manual editing tools for detailed customization and refinement of metabolic maps.
• Integration with constraint-based modeling toolboxes: Integrates with COBRA and COBRApy to visualize simulation results from genome-scale metabolic models.

Scientific Applications:

• KEGG pathway visualization: Visualizes metabolic networks derived from KEGG-annotated pathways.
• Constraint-based model result mapping: Maps simulation outputs from genome-scale constraint-based metabolic reconstructions onto metabolic maps.
• Metabolic engineering analysis: Facilitates evaluation of metabolic engineering strategies by visualizing model-derived simulation results.
• Genetic modification impact assessment: Supports exploration of impacts of genetic modifications by presenting model predictions on metabolic network maps.

Methodology:

Combines automated network partitioning and navigation, manual map editing, and integration with COBRA and COBRApy to visualize genome-scale model simulation results.