NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic...

Area of Science:

• Systems Biology
• Computational Biology
• Metabolic Engineering

Background:

• Genome-scale metabolic network (GSMN) models are crucial for metabolite fate discovery, metabolic engineering, and multi-omics integration.
• Current tools face adoption barriers due to programming complexity, limited visualization, and lack of integrated features.
• Existing software often specializes in either analysis or visualization, missing key functionalities like pathway-specific views and database integration.

Purpose of the Study:

• To present NAViFluX, a unified, web-based tool for metabolic network analysis and visualization.
• To address the limitations of existing tools by integrating pathway map generation, interactive refinement, and comprehensive analyses.
• To facilitate broader adoption of GSMN models by the scientific community.

Main Methods:

• NAViFluX is a web browser-based tool unifying pathway/subsystem map generation and interactive model refinement.
• It integrates with KEGG and BiGG databases for enhanced model accuracy and utility.
• The tool supports flux computations, topological analyses, and functional enrichment directly within network views.

Main Results:

• Demonstrated utility of NAViFluX through three case studies on Escherichia coli.
• Characterized nutrient-specific metabolic adaptations and improved gene essentiality predictions.
• Showcased the rational design of an optimized carbon-fixing metabolic state.

Conclusions:

• NAViFluX offers a comprehensive, visualization-centric approach to metabolic network analysis.
• The tool enhances the interpretability and application of GSMN models for research and engineering.
• NAViFluX facilitates discovery in areas such as metabolic adaptation and synthetic biology design.