Screenshots of the perturbation protocol designer tool. This tool is used to create and edit perturbation protocols. The protocol contains two perturbations. For each perturbation an initial state is described. Each perturbation has one ore more "action" elements, which specify the types of perturbations to be performed. More complex protocols can include other types of actions such as perturbations over a time range or node knockouts. (A) Tree view: contains wizard buttons to add, edit and delete parts of the protocol. (B) Text view: provides a textual representation of the protocol file. Once generated, the protocol file can be saved and re-used.