PORGY

PORGY models biochemical systems using port graphs and rule-based graph rewriting to simulate molecular interactions and analyze dynamic system behavior.

Key Features:

• Port graph representation: Molecules and their interactions are represented as port graphs with nodes for molecular entities and edges for interactions or bindings.
• Port graph rewrite rules: Interactions and transformations are expressed as port graph rewrite rules to enable dynamic simulation of biochemical processes.
• Strategy language: A strategy language controls where, when, and how rewrite rules are applied during simulations.
• State recording and parameter tracking: Model changes are recorded and simulation parameters are tracked over time.
• Parameter plotting: Tracked parameters can be plotted to analyze temporal system dynamics quantitatively.

Scientific Applications:

• Signalling pathway analysis: Simulation and analysis of complex signalling pathways such as the RAF/MEK/ERK cascade.
• Scaffold protein studies: Investigation of scaffold protein roles within signalling networks using rule-based models.
• Systems biology modelling: Modeling dynamic biochemical networks to study system-level behavior in systems biology and bioinformatics.
• Drug discovery support: Analysis of pathway dynamics to inform hypothesis generation relevant to drug discovery.

Methodology:

Models use port graphs (nodes = molecular entities, edges = interactions), define transformations with port graph rewrite rules, control rule application via a strategy language, record state changes and parameters during simulation, and produce parameter plots.