Antigen presentation dynamics shapes the response to emergent variants like the Omicron strain of SARS-CoV-2 after multiple vaccinations with the wild type strain

This repository contains original code created for the study titled "Antigen presentation dynamics shapes the response to emergent variants like the Omicron strain of SARS-CoV-2 after multiple vaccinations with the wild type strain" by Yang, Van Beek, Wang, Muecksch, Canis, Hatziioannou, Bieniasz, Nussenzweig, and Chakraborty in Cell Reports (2023). The raw data from simulations can be downloaded from the following link: https://mitprod-my.sharepoint.com/:u:/g/personal/leerang_mit_edu/EdtAr52PD-5IoVeTmPcYGXEBVk8vmUmOnXmwJ6IIxzIL_A?e=2DlfJh The dataset is very large (111 GB) and exceeds the Mendeley Data storage limit.