PetriNetExhaustiveSimulator

PetriNetExhaustiveSimulator models genetic interaction (GI) patterns using Petri nets (PN) to exhaustively enumerate and analyze four-node mechanisms across three hierarchical levels, generating approximately 5 million simulated models to explain phenotypes of single and double gene mutants, including inversion and suppression patterns.

Key Features:

• Exhaustive Modelling Approach: Defines four-node Petri net models systematically across three hierarchical levels with specific restrictions to explore the space of possible GI mechanisms.
• Simulation Capabilities: Performs large-scale simulations that generate approximately 5 million models and enable identification of GI patterns such as inversion and suppression from pairwise phenotypic data.
• Mechanistic Insights: Generalizes results from exhaustive simulations to propose putative mechanisms underlying observed genetic interaction patterns.
• Versatility in Application: Applies the same Petri net enumeration and simulation methodology to other genetic regulatory datasets beyond pairwise GIs.

Scientific Applications:

• Regulatory mechanism analysis: Investigates complex regulatory mechanisms driving genetic interactions using exhaustive Petri net models.
• Phenotype–genotype interpretation: Elucidates how single and double gene mutations produce observed phenotypes, informing disease pathway and therapeutic target hypotheses.
• Pharmacogenomic exploration: Examines genetic contributions to drug response variability at the level of gene–gene interactions to support personalized medicine research.

Methodology:

Four-node Petri net models are defined and systematically generated across three hierarchical levels with imposed restrictions, and exhaustive large-scale simulations are executed to produce the comprehensive set of approximately 5 million models used to analyze GI phenotypic patterns.