In preparation
This software accompanies the publication
Multiscale modelling of germinal center recapitulates the temporal switch from memory B cells to plasma cells differentiation controlled by antigen affinity-based Tfh cell help.
Elena Merino Tejero, Danial Lashgari, Rodrigo García-Valiente, Xuefeng Gao, Fabien Crauste, Philippe A. Robert, Michael Meyer-Hermann, María Rodríguez Martínez, S. Marieke van Ham, Jeroen E.J. Guikema, Huub Hoefsloot, Antoine H.C. van Kampen
This repository includes code ONLY of the multiscale model of plasma cell diferentiation in Germinal Centers. The Agent-based
model is based on Mafalda, which is based on Hyphasma (e.g., Michael-Meyer Hermann, 2012).
The GRN is based on Martinez et al., 2012. It is posible to simulate 2 scenarios: Plasma cell diferentiation based on
Ag inheritance or on BLIMP1 level.
CD40 signal can be modeled 2 ways: Fixed CD40 (=50, 10) or CD40 dependent on affinity (=affinity*50). The switch from one to the other can be done through parameter file bcinflow09.par. For further information on how to do this see running_specifications.pdf
All software is written in C++
- Martínez, M. R., Corradin, A., Klein, U., Álvarez, M. J., Toffolo, G. M., di Camillo, B., … Stolovitzky, G. A. (2012). Quantitative modeling of the terminal differentiation of B-cells and mechanisms of lymphomagenesis. Proceedings of the National Academy of Sciences, 109(7), 2672–2677.
- Meyer-Hermann, M., Mohr, E., Pelletier, N., Zhang, Y., Victora, G. D., & Toellner, K. M. (2012). A theory of germinal center b cell selection, division, and exit. Cell Reports, 2(1), 162–174.