Cocktail

Cocktail models bacteriophage (phage) infection kinetics in chemostat-like in vitro environments to simulate interactions, growth, and evolution of bacteria and one or two phages using parameterized mathematical formulations.

Key Features:

• Mathematical framework: Represents infection dynamics using a set of coupled differential equations.
• Chemostat environment modeling: Simulates in vitro chemostat-like conditions for continuous-culture dynamics.
• Multiple phage interactions: Supports simulations involving one or two interfering phages.
• Bacterial parameterization: Models bacterial population dynamics with up to sixteen adjustable parameters.
• Phage parameterization: Represents each phage with eight distinct parameters, including adsorption rates and latency periods.
• Biological scenario modeling: Includes parameterized representations of phage resistance mechanisms, metabolically inactive cells, and biofilm formation.
• Dynamic outputs: Produces time-resolved outputs of bacterial and phage population dynamics for analysis and visualization.

Scientific Applications:

• Phage therapy research: Generates hypotheses and indicative guidance for phage therapy by exploring infection kinetics under varied parameter sets.
• Experimental design and interpretation: Supports simulation and interpretation of in vitro chemostat experiments to assess parameter effects on outcomes.
• Co-infection and interference studies: Enables investigation of interactions and interference dynamics between one or two phages.
• Resistance and biofilm investigations: Facilitates exploration of how phage resistance mechanisms, metabolically inactive cells, and biofilm formation alter infection dynamics.

Methodology:

Implements a system of coupled differential equations to represent bacteria and up to two phages in chemostat-like in vitro conditions, with parameterized terms for bacterial dynamics (up to 16 parameters) and phage traits (8 parameters, including adsorption rate and latency).