Kappa - Rule-based language for modeling systems of interacting agents. While its current development is primarily motivated by molecular systems biology, its range of applications is quite broad.
KaSim - Stochastic simulator for rule-based models written in Kappa. KaSa is a static analyser for Kappa models.
BioJulia - Julialang community for biologists and bioinformaticians, working to create great modern software packages for computing with biological data.