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.