Genetic regulatory interactions activate a gene in a way that is often described by a sigmoid function. Already in 1973, Glass and Kauffman showed⁽¹⁾ that a network with this type of interactions can be replaced by a stepwise equivalent. In this 'substitute' network, the activations are approximated to happen switch-like or step-wise, while the outcome of the network behaviour will be the same as the original, continuous one.

This allows us to avoid the use of biochemical balance equations and to use simple stepwise functions instead, as a first approximation.
Following this approach we present to you the SIM-plex simulator with a very user-friendly interface. In its Editor window, you can define each regulatory interaction as one simple if-then statement. When you click on Simulate!, SIM-plex will for each gene combine all the statements that regulate that gene, and translate this into a stepwise activation function in a straightforward and transparent way.

To get started with some examples, please read the tutorial section.

⁽¹⁾ Glass L and Kauffman SA. The logical analysis of continuous, nonlinear biochemical control networks. Journal of Theoretical Biology 39, 103-129 (1973).