STOCHSIM is a stochastic simulator for biochemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. Simple spatial structures can be built.
Basic life is an application that desires to simulate basic life based on some basic chemistry/physics rules. This environment provides particles that can bond, vibrate, react, etc. in order to create basic cells
Python program devoted to study the relationship between cells during inmune response. It is based on a 3D periodic boundary conditions grid where cells see each other and react according to certain movement, growth and interaction rules.