Fluxer

Fluxer computes and visualizes flux graphs from genome-scale metabolic models to analyze metabolic network flux distributions and pathway connectivity.

Key Features:

• Flux Balance Analysis (FBA): Performs Flux Balance Analysis on genome-scale models to calculate steady-state flux distributions.
• SBML support: Accepts models formatted in Systems Biology Markup Language (SBML) for analysis.
• Flux distribution computation: Calculates flux distributions within metabolic networks to reveal metabolite flows through biochemical pathways.
• Visualization methods: Generates spanning trees, dendrograms, complete graphs, and k-shortest path visualizations of metabolic networks.
• K-shortest paths computation: Computes and visualizes k-shortest paths between specified metabolites or reactions to identify principal metabolic routes.
• Gene knockout simulation: Simulates gene knockouts within major metabolic pathways to assess effects on network functionality and fluxes.
• Pre-loaded reconstructions: Includes a database of over 80 whole-genome metabolic reconstructions spanning bacteria to humans.
• Next-generation sequencing: Leverages advancements in next-generation sequencing technologies as part of its analytical context.

Scientific Applications:

• Flux analysis: Quantitative analysis of metabolic flux distributions using FBA on SBML models.
• Pathway identification: Identification of critical routes for biomass growth or biosynthesis of specific metabolites.
• Route discovery: Discovery of metabolic pathways by computing k-shortest paths between compounds or reactions.
• Perturbation studies: Assessment of the impact of gene knockouts on network functionality and metabolic fluxes.
• Comparative network analysis: Comparative analysis of metabolic networks across organisms using the included whole-genome reconstructions.

Methodology:

Performs Flux Balance Analysis (FBA) on SBML-formatted genome-scale models; computes flux distributions and k-shortest paths between metabolites or reactions; generates spanning trees, dendrograms, and complete graphs for network representation; and simulates gene knockouts to evaluate effects on fluxes.