The Microbiome Multiscale Modeling Project is a research-focused endeavor aimed at building a multiscale understanding of microbiome through the development and refinement of metabolic analysis techniques. Our focus is on a system-level understanding, using computational models to shed light on the complex processes that define the interactions within microbial communities. The project employs the Vivarium framework, a tool designed to support the construction and simulation of complex biological systems model.
We began the project with the implementation of Flux Balance Analysis (FBA) for Escherichia coli, a well-studied model organism. FBA is a mathematical procedure used for simulating the metabolism of biological organisms.
Building on our initial implementation, we implemented to Dynamic Flux Balance Analysis (dFBA). dFBA is a time-resolved extension of FBA, capable of modeling the flux at each time-step. This advancement enables us to capture and analyze the time-dependent behavior of the E. coli's metabolism within the simulated environment.