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Birch, E. W., Ruggero, N. A., & Covert, M. W. (2012). Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation. PLoS Computational Biology, 8(10), e1002746. doi:10.1371/journal.pcbi.1002746 (2012)
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Provides the simulation code used in published integration of phage T7 ODEs and E. coli FBA.

License: t7phagefba

The associated publication described the integration of T7 phage viral replication Ordinary Differential Equations with host E. coli metabolic Flux Balance Analysis such that the two models interact and constrain one another over the time course of infection and virion synthesis. This code runs the simulations and produces the results figure panels in the publication.

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Provides: the flat files and model specific functions describing the particular models used (.text and MatLab formats); the modular and generalizable functions defining the simulation integration method developed (MatLab formats); and the parsers and visualization functions (MatLab formats and R) that produce the publication associated figures.

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