#30 · Tools & infrastructure

Compiler-verified and formal languages for executable laboratory protocols

The dominant thread is machine-checkable representation of laboratory protocols. BPL specifies biology protocols in a compiler-verified language with unit-aware types, and BPL-COGEN pairs a fine-tuned LLM with a compiler repair loop to produce protocols that pass these checks. Culsma takes a related route as an executable specification language in which each operation is defined by its effect on experimental state, so protocols become programs that can be machine-checked. What is new is the explicit verification layer, whether compiler checks or formal state-change semantics. plyxp is a separate contribution at the data-manipulation layer, an R/Bioconductor grammar for tidy handling of annotated matrix data such as gene expression counts, and it does not address protocol verification. The summaries provided do not describe evaluation of predictive generalization under distribution shift.