From 18cdabc7581f03ab9b2aa978ed06676ef9784ff5 Mon Sep 17 00:00:00 2001 From: "Cody, Jonathan William" Date: Mon, 15 May 2023 11:34:56 -0500 Subject: [PATCH] Update README.md --- README.md | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index a1041db..1bbd75c 100644 --- a/README.md +++ b/README.md @@ -1,34 +1,36 @@ # N-803_SIV_Model Jonathan W. Cody -This repository contains all the code needed to replicate the following journal article, soon to be submitted to PLoS Computational Biology. MATLAB R2018b or later is required. +This repository contains all the code needed to replicate the following journal article, submitted to PLoS Computational Biology. MATLAB R2018b or later is required. Cody JW, Ellis-Connell AL, O’Connor SL, Pienaar E. "Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load." ========================= -To replicate the article, unzip the entire repository into a folder and run the code in the following order below. Steps #1,2 are lengthy (~1 week each). Results of step #3 are included in the repository in the file 'N803_MCMC.mat', which allows you to skip to plotting (steps #4,5). +To replicate the article, unzip the entire repository into a folder and run the code in the following order below. Results of step #3 are included in the repository in the file 'N803_ForPlots.mat', which allows you to skip to plotting (steps #4,5). - 1. "main_shared_calibration_2022_08_18.m" (runs MSLS and MCMC for both cohorts with parameters shared) + 1. "main_shared_2_calibration" (runs MSLS and MCMC for both cohorts with shared constants) 2. "main_singles_calibration_2022_09_25.m" (repeat with parameters not shared) 3. "N803_collector_2.m" (stores model outputs, parameters, and initial conditions from thinned MCMC sample) 4. "N803_plotter_2.m" (creates all time-course plots) - 5. "N803_plotter_2_parameters.m" (creates parameter violin plots) + 5. "N803_plotter_2_violin.m" (creates violin plots) ========================= The repository containts the following data (MATLAB .mat files): -"N803_DataSet_1.mat" (Cohort 1 calibration data) +'N803_DataSet_1.mat' (Cohort 1 calibration data) Source: Ellis-Connell AL, Balgeman AJ, Zarbock KR, Barry G, Weiler A, Egan JO, et al. "ALT-803 Transiently Reduces Simian Immunodeficiency Virus Replication in the Absence of Antiretroviral Treatment." Journal of virology. 2018;92(3). -"N803_DataSet_2.mat" (Cohort 2 calibration data, validation data) +'N803_DataSet_2.mat' (Cohort 2 calibration data, validation data) Source: Ellis-Connell AL, Balgeman AJ, Harwood OE, Moriarty RV, Safrit JT, Weiler AM, et al. "Control of Simian Immunodeficiency Virus Infection in Prophylactically Vaccinated, Antiretroviral Treatment-Naive Macaques Is Required for the Most Efficacious CD8 T Cell Response during Treatment with the Interleukin-15 Superagonist N-803." Journal of virology. 2022;96(20). -Webb_DataSet.mat" (validation data) +'Webb_DataSet.mat' (validation data) Source: Webb GM, Li S, Mwakalundwa G, Folkvord JM, Greene JM, Reed JS, et al. "The human IL-15 superagonist ALT-803 directs SIV-specific CD8(+) T cells into B-cell follicles." Blood advances. 2018;2(2):76-84. -'N803_MCMC.mat' (model parameter values, initial conditions, and outputs underlying all article figures) +'mean_data' (mean across individuals of Ellis-Connell data at each time point; used in supplemental figure S7) + +'N803_ForPlots.mat' (model parameter values, initial conditions, and outputs underlying all article figures) =========================