bio-systems-biology-network-visualization

What problem does it solve?

This Skill removes the friction of integrating multiple tools to create clear, publication-ready metabolic network visualizations and to overlay quantitative flux or metabolomics data onto pathway maps.

Core Features & Use Cases

• Escher overlays: render FBA flux distributions or metabolite concentration dictionaries onto Escher pathway maps for interactive exploration.
• Cytoscape automation: programmatically build networks, apply layouts, map continuous and discrete data to visual properties, and export high-resolution images or sessions via py4cytoscape.
• KEGG integration: fetch pathway membership and color KEGG pathway diagrams by gene or compound values using the KEGG REST API.
• Network analysis with NetworkX: construct metabolite- or reaction-centric graphs from COBRA models, compute centrality metrics, remove currency metabolites, and generate publication-quality static figures.
• Use case: compare aerobic vs anaerobic FBA runs, compute flux differences, visualize deltas on Escher with diverging color scales, and export HTML/SVG for manuscripts.

Quick Start

Render an Escher map of FBA fluxes from a COBRApy model and save the result as an interactive HTML file.