Webpages about Smoldyn and spatial simulation

Choosing appropriate simulation parameters for a model is always a challenge. It is particularly challenging for highly detailed simulations, such as those that Smoldyn does, because these simulations require more parameters than others do. In addition, most necessary parameters have not been measured experimentally.

However, parameterizing models is not as daunting as it might seem. The notes section of this Methods in Molecular Biology paper (pdf) offers several suggestions.