BioNSi

BioNSi simulates biological networks in discrete time to analyze pathway-level dynamics and integrate experimental expression data.

Key Features:

• Discrete-time network simulation: Simulates dynamic behavior of biological networks using discrete time steps for pathway-level analysis.
• KEGG pathway integration and merging: Imports multiple KEGG pathways and merges them into a single unified network model to support network construction.
• Parameterization: Allows assignment of parameter values to network components to configure model dynamics.
• Experimental expression data integration: Incorporates experimental expression data into network models to drive simulations under specific biological conditions.
• Simulation of perturbations and conditions: Simulates network responses to disease states and treatment interventions, with reported applications to inflammatory bowel disease and breast cancer treatment.

Scientific Applications:

• Systems biology and pathway analysis: Enables pathway-level investigation of network dynamics and interactions.
• Hypothesis testing and validation: Facilitates in silico evaluation of hypotheses by combining models with experimental expression data.
• Investigation of disease mechanisms and therapeutics: Supports exploration of disease-state behaviors and assessment of treatment effects, including studies of inflammatory bowel disease and breast cancer treatment.

Methodology:

Merging KEGG pathways into a unified network model, parameterizing network components, loading experimental expression data, and simulating discrete-time network dynamics.