compuGUT

compuGUT simulates interactions between intestinal microbiota and their environment to model colonic ecosystem dynamics.

Key Features:

• Numerical simulation: Core numerical computations are implemented in C for performance and accuracy.
• Scripting support: Accessory scripts in Bash (for Linux) and R are provided for data loading and visualization.
• Integration libraries: The SUNDIALS libraries are employed for numerical integration of the model equations.
• Interactive visualization: GoogleVis API is used to produce interactive visualizations of simulation results.
• Mathematical model: A defined mathematical framework captures the essential dynamics of microbiota interactions in the colon.
• Numerical analysis: Supplementary materials include characterization of numerical errors and computing times for implementation parameters.

Scientific Applications:

• Anaerobic Digestion: Simulating microbial processes relevant to anaerobic digestion and waste treatment.
• Large Intestine Research: Modeling the ecological dynamics of the human large intestine microbiota.
• Mathematical Modeling: Providing a computational platform for developing and testing theoretical models of microbiota behavior.

Methodology:

Numerical computations implemented in C use SUNDIALS for integration; Bash and R scripts handle data loading and visualization with GoogleVis; supplementary materials document the mathematical framework and numerical error and computing time characterizations.