modelbase

modelbase provides dynamic mathematical modeling for systems biology, enabling construction, analysis, and simulation of ODE-based models with SBML interoperability and isotope-specific expansions.

Key Features:

• Model construction and analysis: Automatically generates the system of ordinary differential equations from reaction stoichiometries and specified rate equations.
• Unified kinetic rate laws library: Includes a comprehensive library of common kinetic rate laws to standardize and reuse reaction formulations.
• Enhanced visualization capabilities: Provides visualization methods for both structural and dynamic properties of models.
• Compatibility with SBML: Supports Systems Biology Markup Language (SBML) for model import and export to ensure interoperability.
• Isotope labeling support (v1.2.3): Streamlines expansion of classical models to isotope-specific versions using user-provided label maps to simulate label propagation and analyze network topology and metabolic fluxes.
• Growing library of models: Maintains a repository of previously published models in a unified format covering processes such as photosynthesis, tumor cell growth, and viral infection evolution.

Scientific Applications:

• Regulatory processes: Simulate and analyze dynamic behavior of regulatory networks using ODE-based formulations.
• Metabolic flux analysis: Study metabolic fluxes and tracer experiments via isotope-specific model expansions and label propagation simulations.
• Drug therapy effects: Model the dynamic effects of drug interventions on biochemical and cellular systems.
• Disease dynamics and evolution: Investigate disease-related dynamics including tumor cell growth and viral infection evolution.
• Model reuse and extension: Reuse, adapt, and extend published systems biology and systems medicine models in a unified representation.

Methodology:

Assembles ODE systems from reaction stoichiometries and rate equations, applies a library of kinetic rate laws, supports SBML import/export, expands models to isotope-specific versions using user-provided label maps to simulate label propagation, and produces visualizations of structural and dynamic model properties.