GeNeTool is designed to compute Boolean gene expression in time and space as an output of gene regulatory interactions, including under conditions in which these interactions are perturbed, either exper- imentally or purely in silico. Your starting point for use of GeNeTool will be a gene regulatory network (GRN) consisting of a set of regulatory genes plus the regulatory interactions between them. If this GRN is based on experimental data, then GeNeTool will allow you to compare the gene expression that it computes using information derived from your GRN model to the observed expression of the same genes. GeNeTool can also be used to test purely theoretical network architectures for their spatial and temporal expression outputs.