Abstract
Recent next generation sequencing and single molecule methodologies provide functional insights into gene regulatory networks beyond Boolean interactions, including the number, binding modes and kinetic rates of transcription factors and the kinetics of gene bursting. We report CaiNet, a fast computer aided interactive network simulation environment to set up and simulate arbitrary gene regulatory networks. CaiNet automatically compiles a network laid out in a graphical user interface into a fast hybrid stochastic-deterministic simulation framework without further mathematical knowledge or input by the user. Stochastic noise can optionally be omitted for simplified deterministic solutions. We validate CaiNet by comparison with Gillespie simulations using an auto feedback motive. We apply CaiNet to the circadian clock and find that temporally modulated external input signals allow regulating the periodicity of oscillations in a nested network topology. We further use CaiNet to simulate the temporal behavior of the pluripotency network, using published kinetic parameters where possible, as it transits from the naïve state to germ layer lineages upon changes in signal inputs.