the homepage of the simulator that lets you define a genetic network
while avoiding complex biochemical differential equations!
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
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
To get started with some examples, please read the tutorial section.
Glass L and Kauffman
SA. The logical analysis of continuous, nonlinear biochemical
control networks. Journal of Theoretical Biology 39, 103-129