The Mindscope project at the Allen Institute aims to elucidate mechanisms underlying cortical function in the mouse, focusing on the visual system. This involves concerted efforts of multiple teams characterizing cell types, connectivity, and neuronal activity in behaving animals. An integral part of these efforts is the construction of models of the cortical tissue and cortical computations. To achieve this, multi-model experimental data are integrated into a highly realistic 230,000-neuron model of the mouse cortical area V1. We perform systematic comparisons of simulated responses to in vivo experiments and investigate the structure-function relationships in the models to make mechanistic predictions for experimental testing. To enable this work, we developed the software suite called Brain Modeling ToolKit (BMTK) and a modeling file format called SONATA. These tools, the models, and simulation results are all being made freely available to the community via the Allen Institute Modeling Portal.