CellNetAnalyzer

CellNetAnalyzer performs structural and functional analysis of cellular networks, supporting mass-flow (metabolic) and signal-flow (signaling and regulatory) network modeling and qualitative prediction of perturbation effects.

Key Features:

• Structural Analysis: Parameter-free structural and topological analyses that characterize functional states, detect dependencies, identify intervention strategies, and predict qualitative effects of perturbations.
• Metabolic Network Analysis: Stoichiometric and constraint-based modeling capabilities including metabolic flux analysis, flux balance analysis (FBA), flux variability analysis (FVA), and computation of elementary flux modes.
• Signal-Flow Network Analysis: Analysis of interaction graphs to compute shortest positive and negative paths and circuits and identification of minimal intervention sets in logical networks.
• Computational Strain Design: Methods to propose genetic modifications aimed at maximizing production performance in microbial systems.

Scientific Applications:

• Systems Biology: Structural and qualitative analysis of metabolic, signaling, and regulatory networks to study cellular organization and behavior.
• Metabolic Engineering: Use of constraint-based and flux analysis methods to design and evaluate modifications for improved biochemical production.
• Bioprocess Optimization: Application of flux analyses and elementary flux mode computations to optimize production performance in microbial systems.
• Regulatory and Signaling Network Analysis: Identification of paths, circuits, and minimal intervention sets to investigate regulatory mechanisms and control strategies.

Methodology:

Methods explicitly include structural/topological analysis and parameter-free methods to characterize functional states, detect dependencies, identify intervention strategies and predict perturbation effects; stoichiometric and constraint-based modeling including metabolic flux analysis, flux balance analysis and flux variability analysis; computation of elementary flux modes; computation and analysis of shortest positive and negative paths and circuits in interaction graphs; and identification of minimal intervention sets in logical networks.