STEPS workflow. The biochemical model and the geometry are described separately (using Python modules steps.model and steps.geom respectively) and are brought together by the solver object. The steps.utilities namespace contains various helper modules that assist in model and geometry construction. Python packages such as SciPy are a convenient tool for post-simulation analysis.
Hepburn et al. BMC Systems Biology 2012 6:36 doi:10.1186/1752-0509-6-36