starlogo nova (requires flash plugin) is a relatively simple agent-based programming language to develop e.g. biology / chemistry simulations.
epidemic (2-D)
ecology (2-D)
AgNO3 + Cu (2-D)
AgNO3 + NaCl (2-D)
version 2.0: + gravity; - graph
AgNO3 + NaCl (2-D)
version 2.1: - gravity; + graph
The first 4 simulations were assignments in an online course (Dec 2014 - Jan 2015) about teaching computer science concepts in a science course; course videos.
Other teachers' website