In August 2011, a week-long NSF-sponsored workshop focusing on the Tree of Life (ToL) took place in Lake Placid, New York. This workshop, called AVAToL (Assembling Visualizing, and Analyzing the Tree of Life), was the first application of NSF’s Ideas Lab concept to systematics. In this article we outline the history and motivation for the Ideas Lab approach and its application to the ToL, explain the nuts and bolts of the Ideas Lab process and look to the potential contributions of AVAToL funded projects to help enable the future of ToL and more broadly, comparative biological research.