DESCRIPTION:
Stochastic model of the immune response to dengue infections and effect of vaccination. This model is designed to simulate the human response of B cell and T cells to the dengue virus and to the polyvalent live-attenuated vaccine constructs. The immune system is modeled as a system of chemical reactions using the Gillespie algorithm (Woo & Reifman, Proc Nat Acad Sci USA, 2012). It uses the immune shape space model developed by Smith et al. (Smith et al., J Theor Biol 1997) and the immune response model by B cells for malaria by Chaudhury et al. (Journal of Immunology. 2014).
REQUIREMENTS: The immune modeling code requires Python 2.4 or later.
USAGE EXAMPLES:
Natural infections:
python run_dengueinfections.py <data_file> monovalent
python run_dengueinfections.py <data_file> polyvalent
Vaccine studies:
python run_infectvaccine_vaccineDENV2.py <data_file> polyvalent monovalent
python run_infectvaccine_3vaccinesDENV2.py <data_file> polyvalent monovalent
CITATION:
Nguyen et al. Stochastic models of the adaptive immune response predict disease severity and captures enhanced cross-reactivity in natural dengue infections. Journal of Immunology. 2021