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CART PKPD model

This code is for my AM 881 (Introduction to Mathematical Oncology) final project. The code replicates and analyzes the PKPD model presented in Kirouac et al., Nature Biotechnology, 2023.

Key files

  • mod_eqns model equations
  • driver_allpatients.m Run simulations for all the VPs presented in Kirouac et al., 2023. Model results are saved to directory "sims_patients"
  • plot_allpatients.m Plot the results from driver_allpatients.m. This is used to make Fig. B.1, B.2, and B.3
  • parameter_PCA.m conduct PCA and plot results for the 36 VPs from Kirouac et al., 2023. This is used to make Fig. B.4 and B.5
  • param_hists.m Loads and creates histograms of the parameters for the 36 VPs from Kirouac et al., 2023. This is used to make Fig. B.6, B.7, B.8
  • generateVPparams.m Generates parameter set for VPs. Results are saved to directory "VP"
  • simulateVP.m Simulate CART therapy for each VP in the VP set generated from generateVPparams
  • sortVP.m Creates labels for each of the VP based on the simulation results. NOTE: This requires the directory VPsims (see below) or will need to conduct simulations using simulateVP.m first.
  • VP_paramPCA.m Conduct PCA on the VP population results. Makes Fig. C.1.
  • VPparams_hist.m Conducts ANOVA test for each parameter and plots a histogram of the values for diverges, responders, and non-responders. Makes Fig. C.2 and C.3 - C.8

VP simulation data

The VP simulation data directory VPsims has been uploaded to https://figshare.com/articles/dataset/VP_simulations_for_CART_project/25612824. This is required to run "sortVP.m".