The efficacy of a newly created software package for predictive modeling of developmental gene regulatory networks (GRNs) has recently been demonstrated (Peter et al., 2012). The program GeNeTool computes spatial gene expression patterns based on GRN interactions and thereby allows the direct comparison of predicted and observed spatial expression patterns. GeNeTool also permits in silico exploration of both cis-and trans-perturbations of GRN interactions. Here, we present this program, review briefly its major features and applications, and provide a detailed and accessible tutorial.