PyDSTool

PyDSTool provides a programmatic environment for developing, simulating, and analyzing dynamical systems models with emphasis on biological and biophysical applications.

Key Features:

• Programmatic Environment: Provides a flexible programming interface for building and iteratively refining models based on experimental data and emerging hypotheses.
• Support for Various Dynamical Systems Models: Implements and simulates ordinary differential equations (ODEs), differential-algebraic equations (DAEs), discrete maps, and hybrid systems.
• Hybrid Dynamical Modeling: Supports hybrid dynamical models for reverse engineering complex biophysical dynamics, exemplified by modeling excitable membranes.
• Inference and Validation Tools: Includes tools to infer and validate mechanistic hypotheses by integrating quantitative and qualitative data constraints.
• Simulation and Analysis: Enables simulation and analysis of dynamical behavior for model exploration and hypothesis testing.

Scientific Applications:

• Reverse engineering biophysical systems: Construction and validation of mechanistic models to reverse engineer complex dynamics such as excitable membranes.
• Exploratory data- and hypothesis-driven modeling: Integrating experimental constraints to test and refine mechanistic hypotheses in biological research.

Methodology:

Development, simulation, and analysis of dynamical systems models including ODEs, DAEs, maps, and hybrid systems; hybrid dynamical modeling for reverse engineering; and inference/validation methods that integrate quantitative and qualitative data constraints.