BioModME

BioModME builds and simulates dynamic computational models of complex biological systems.

Key Features:

• Multi-region system modeling: Supports modeling across multiple spatial or compartmental regions.
• Custom reaction rate laws and equations: Allows users to define bespoke kinetic expressions and mathematical equations.
• Unit conversion: Performs automatic or manual conversion of measurement units within models.
• Model parameter estimation: Estimates parameters by fitting models to experimental data.
• Systems Biology Markup Language import and export: Enables model exchange in SBML format.
• Code export: Exports models to MATLAB, R, and Python languages.
• Equation export: Exports equations to LaTeX and Mathematical Markup Language formats.
• Multi-modality visualization: Provides diverse visualization capabilities for model outputs.
• Numerical solvers: Implements efficient solvers for differential-algebraic equations and optimization.

Scientific Applications:

• Computational modeling of biological functions: Investigates molecular mechanisms underlying normal biological processes.
• Disease process modeling: Interrogates and understands relationships in pathological mechanisms.
• Model-based data analysis: Fits computational models to experimental data for parameter inference and hypothesis testing.

Methodology:

BioModME employs numerical solvers for differential-algebraic equations and optimization algorithms for parameter estimation.