Performance modeling typically relies on two antithetic methodologies: white box models, which exploit knowledge on system's internals and capture its dynamics using analytical approaches, and black box techniques, which infer relations among the input and output variables of a system based on the evidences gathered during an initial training phase. In this paper we investigate a technique, which we name Bootstrapping, which aims at reconciling these two methodologies and at compensating the cons of the one with the pros of the other. We thoroughly analyze the design space of this gray box modeling technique, and identify a number of algorithmic and parametric trade-offs which we evaluate via two realistic case studies, a Key-Value Store and a Total Order Broadcast service.