Vivarium-COMETS is a multiscale modeling project that leverages the capabilities of the Vivarium package to implement the COMETS methodology. This project aims to provide a comprehensive framework for simulating and analyzing complex microbial systems in spatial environments, enhancing our understanding of dynamic interactions within various environments.
- Implementation of the COMETS Methodology Using Vivarium: Utilizes the robust features of Vivarium to bring the COMETS methodology to life. The model comprehensively simulates both the environment and the microorganisms within it.
- Analysis and Visualization Capabilities: Includes advanced capabilities for analyzing system interactions, with a focus on Flux Balance Analysis (FBA). This allows for the detailed examination and visualization of metabolic fluxes within the system, facilitating a deeper understanding of the underlying biological processes.
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Diffusion notebook: Demonstrates simulating and visualizing molecular concentrations in a 2D field influenced by diffusion, advection, and sinking.
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Spatial dFBA notebook: This Jupyter notebook models the dynamic metabolic behavior of microorganisms over time using dynamic Flux Balance Analysis (dFBA). It performs flux balance analysis for each organism in the field at each timestep, computes the exchange fluxes, and updates the field based on these fluxes.
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VivaComets Notebook: The VivaComets notebook integrates the functionalities of two previously developed notebooks to create a comprehensive simulation environment. This combined notebook accounts for the diffusion and advection of molecules and species biomass within a 3D environment. Additionally, it performs dynamic Flux Balance Analysis (dFBA) for organisms in this spatially structured environment.
Key Features:
Diffusion and Advection: Models the movement and distribution of molecules and biomass through diffusion and advection processes, simulating realistic environmental interactions.
Dynamic Flux Balance Analysis (dFBA): Computes the growth and metabolic rates of organisms dynamically over time, considering the spatial distribution of resources and environmental conditions.
2D Environment: Simulates the interactions and growth of multiple species in a two-dimensional space, providing a more realistic and detailed analysis of ecological and metabolic dynamics.
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