Code to run the model described in Bistodeau-Gagnon, Segal, Craig, and Michaels.

System requirements

All of the code was written and tested using MATLAB R2025b. The following toolboxes are required:
- Optimization Toolbox
- Statistics and Machine Learning Toolbox
- Symbolic Math Toolbox

Installation guide

Download all the files in this repository. The typical install time is < 1 min.

Demo and instructions for use

Each folder contains the code necessary to reproduce all the figures. Each folder can be run independently of the other.
In the code, it is worth mentioning that we refer to D7 as the T cell differentiation stage and D14 as the T cell maturation stage, as per Michaels et al., 2021 (10.1126/sciadv.abn5522). Cells types for iPSCs are denoted as follows:
PROT: ProT cells
CD4ISP: CD4 single positive cells
CD3N: Double positive CD3- cells
CD3P: Double positive CD3+ cells
SP: CD8 single positive cells
For the cord blood-derived cells are denoted as follows: CD7pCD5n: CD7+CD5- cells CD7pCD5p: CD7+CD5+ cells For the cord blood-derived cells, the different donors are noted as "vials". In each folder for figures and supplementary figures, run file containing "commands" in the title to execute the code. When necessary, a folder “Figures” is included in the folder to store results files (.m files) and figures (in PDF). The expected run time for each folder is <10 min.

Data

The data analyzed in this study were obtained from a publicly available source (10.1126/sciadv.abn5522, Tables S1-S7). The iPSC folder contains all the cytokine concentrations in ng/mL and the polynomial coefficients for the dose-responses from Michaels et al. (2022). We also used data generated from experiments tailored to this specific study (contained in file Cord Blood with the code).