In review
This software is currently under review and the API may change before its final release.Welcome to SimBLE!
SimBLE is a BCR evolution simulator. It starts with a naive heavy and light chain pair, and models evolution and selection in the germinal center as well as migration out of germinal center. SimBLE also has customizable sampling.
How SimBLE works
SimBLE is an agent-based simulator of heterogenous evolution, specializing in B cell evolution and differentiation in germinal centers (GCs). Briefly, a starting pair of BCR heavy and light chain sequences is randomly chosen from a dataset of naive single B cells. GC B cells mutate according to models of SHM (somatic hypermutation) targeting, and affinity is calculated based on similarity to a target amino acid sequence. B cells proliferate proportionally to their relative affinity. GC B cells differentiate into memory B cells (MBCs) early on before shifting to mainly plasma cell production. SimBLE incorporates recently discovered aspects of GC reactions, including transient silencing of SHM during clonal bursts and a log-additive relationship between mutations and affinity.
Contact
If you need help or have any questions, please contact the Hoehn Lab.
If you have discovered a bug or have a feature request, you can open an issue using the issue tracker.
Citing
To cite the SimBLE package in publications, please use:
Fielding J, Wu S, Melton H, Du Plessis L, Fisk N, Hoehn K (2025). “TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations.” bioRxiv 2025.10.21.683591 doi:10.1101/2025.10.21.683591 https://doi.org/10.1101/2025.10.21.683591
License
AGPL-3