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bio-systems-biology-network-visualization

Visualize metabolic networks and overlay flux data onto pathway maps.

7|Updated Apr 5, 2026
Search Tags:#networkx#kegg#cytoscape#fba#metabolic-network#flux-visualization#escher
One-click install
npx skills add https://github.com/dailycafi/metabolism-skills --skill bio-systems-biology-network-visualization
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-systems-biology-network-visualization
Source: https://github.com/dailycafi/metabolism-skills/tree/main/skills/systems-biology/network-visualization
Command: npx skills add https://github.com/dailycafi/metabolism-skills --skill bio-systems-biology-network-visualization

SYSTEM DOCUMENTATION & REQUIREMENTS

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.

Frequently Asked Questions about bio-systems-biology-network-visualization

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I visualize FBA flux distributions on an Escher pathway map?▼

To visualize FBA flux, you overlay quantitative flux data from a COBRApy model onto an Escher pathway map and export the result as an interactive HTML file for exploration.

What is the best way to automate Cytoscape network layouts programmatically?▼

Automating Cytoscape network layouts is done via py4cytoscape to programmatically build networks, apply layouts, map data to visual properties, and export high-resolution images.

Can I compute centrality metrics for a metabolic network using NetworkX?▼

Yes, you can construct metabolite- or reaction-centric graphs from COBRA models using NetworkX to compute centrality metrics, remove currency metabolites, and generate static figures.

Do I need a running Cytoscape instance to use this metabolic network visualization workflow?▼

Yes, a running Cytoscape instance is required for remote automation when using this workflow to programmatically build networks and export images via py4cytoscape.

How do I compare aerobic vs anaerobic FBA runs on a pathway map?▼

To compare aerobic vs anaerobic FBA runs, you compute flux differences and visualize the deltas on an Escher map using diverging color scales, then export the results as HTML or SVG.

How do I color KEGG pathway diagrams by gene or compound values?▼

You color KEGG pathway diagrams by fetching pathway membership via the KEGG REST API and mapping gene or compound values onto the pathway diagrams for visualization.

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