This repository contains scripts and materials to reproduce the results in the publication "Dynamic metabolic modeling of ATP allocation during viral infection" by Alvin Lu, Ilija Dukovski, Daniel Segrè (https://www.biorxiv.org/content/10.1101/2024.11.12.623198v1). It requires the software COMETS and its interface COMETSpy which can be downloaded from https://www.runcomets.org, and the code can be found at https://github.com/segrelab/comets and https://github.com/segrelab/cometspy.
The respository is organized by figures:
FluxComparer compares the fluxes between the model with and without lipids. It uses ReactionLabels' data to categorize reactions and generate Figures 4 and 5.
VirusRunner is the main notebook that sets up a SARS-CoV-2 infected macrophage experiment (including partitioning ATP and enabling host maintenance). It graphs the virus growth and host death over time. DynamicModelGrapher synthesizes data generated from VirusRunner with different partition ratios.
PartitionRatioRunnerC compares generates data about virus biomass and host lifespan based on different partition ratios and a set host maintenance. GrapherC reads and plots the data.
PartitionRatioRunnerB compares generates data about virus biomass and host lifespan based on different partition ratios and different host maintenance values. GrapherB reads and plots the data.
HostKnockout and VirusKnockout generate data about host/virus flux for each gene knockout. KnockoutComparer then determines potential drug targets based on those data. PartialKnockout tries 10% and 50% knockout on those potential drug targets to further test their efficacy.
