BEL2ABM

BEL2ABM converts Biological Expression Language (BEL) models into dynamic, executable agent-based simulations to introduce temporality and continuous dynamics for mechanistic hypothesis generation.

Key Features:

• Dynamic Model Generation: Transforms static BEL representations into continuous, time-resolved models that represent temporal dynamics.
• Agent-Based Simulation: Implements agent-based modeling (ABM) to simulate interactions among individual agents and emergent system behavior.
• Integration with BEL Templates: Leverages existing BEL templates to preserve and extend mechanistic knowledge during model conversion.
• Development Environment: Implemented using Java and NetLogo for model construction and execution.

Scientific Applications:

• Mechanistic hypothesis generation: Facilitates exploration and validation of mechanistic hypotheses by simulating temporal system behavior derived from BEL knowledge.
• Systems biology: Enables dynamic investigation of complex biological networks and their emergent properties over time.
• Pharmacology and drug response modeling: Supports simulation of time-dependent drug effects and response dynamics within mechanistic network contexts.
• Personalized medicine and disease mechanism investigation: Allows study of disease mechanisms and time-dependent biological phenomena informed by BEL-encoded mechanistic relationships.

Methodology:

Converts static BEL models into agent-based frameworks to simulate continuous temporal processes while retaining BEL mechanistic relations, with implementations in Java and NetLogo.