MpTheory

MpTheory models observed biological dynamics using Metabolic P (MP) theory to enable construction and inference of discrete and continuous-time MP models from time-series data.

Key Features:

• Modeling Capabilities: Implements MP theory through a collection of Java objects and algorithms to represent dynamic biological systems.
• Regression Algorithms: Provides regression methods specifically aimed at inferring MP models from time series data.
• Continuous and Discrete Time Support: Supports construction and analysis of models that operate in both continuous and discrete time intervals.
• P Systems Representation: Uses P systems as the computational model to represent metabolic processes and dynamic interactions.
• Cross-Platform Integration: Supports integration with MATLAB, GNU Octave, Mathematica, and R in addition to the core Java implementation.

Scientific Applications:

• Systems Biology Modeling: Enables modeling of metabolic and other dynamic biological processes within a discrete mathematical framework.
• Time-Series Inference: Facilitates extraction of MP models from observational time-series data to analyze system dynamics.
• Simulation of Dynamic Processes: Allows simulation and analysis of biological dynamics across continuous and discrete temporal settings and diverse experimental conditions.

Methodology:

Implements Metabolic P (MP) theory as a discrete mathematical framework, uses P systems for computational representation of metabolic processes, and applies regression algorithms to infer MP models from time-series data.