Modeling Genome Evolution with a DSEL for Probabilistic Programming

Abstract

Abstract. Many scientific applications benefit from simulation. However, programming languages used in simulation, such as C++ or Matlab, approach problems from a deterministic procedural view, which seems to differ, in general, from many scientists' mental representation. We apply a domain-specific language for probabilistic programming to the biological field of gene modeling, showing how the mental-model gap may be bridged. Our system assisted biologists in developing a model for genome evolution by separating the concerns of model and simulation and providing implicit probabilistic non-determinism.