Numerous methods have been developed for inference of gene regulatory networks from expression data, however, their strengths and weaknesses remain poorly understood. Accurate and systematic evaluation of these methods is hampered by the difficulty of constructing adequate benchmarks and the lack of tools for a differentiated analysis of network predictions on such benchmarks. We present the new version (3.0) of GeneNetWeaver (GNW), an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW can be launched directly from any web browser thanks to the deployment technology Java Web Start.