RuleBender

RuleBender facilitates integrated visualization, modeling, and simulation of rule-based intracellular biochemistry.

Key Features:

• Rule-based model creation and debugging: Supports creation and debugging of rule-based models to specify biochemical interactions.
• Interactive visualization: Provides interactive visualization of rule-based models to inspect model structure and rules.
• Built-in simulation execution: Includes built-in simulation capabilities to execute simulations directly from models.
• Multiple linked views for analysis: Analyzes simulation results through multiple linked views.
• Global and local model exploration: Enables visual exploration of models at both global and local levels of detail.
• Network generation and analysis: Generates networks from rule-based models and supports analysis of the generated networks.
• Error minimization in model specification: Aims to reduce errors during model specification.

Scientific Applications:

• Rule-based modeling of cell signaling networks: Represents and studies cell signaling networks using rule-based modeling (RBM).
• Simulation of intracellular biochemistry: Simulates intracellular biochemical processes to analyze dynamic behavior.
• Structure–dynamics exploration of biochemical networks: Investigates relationships between network structure and dynamic outcomes at multiple scales.

Methodology:

Creation and debugging of rule-based models, interactive and linked visualizations, built-in simulation execution, and generation and analysis of networks.