In this paper we describe a Multi-Agent Bioinformatics Integration System that aims at helping users make the most of the available integration facilities while also increasing their trust in the system. To this end, an explanation facility that helps the users to better understand how the system has arrived at a particular answer is provided. This is especially useful when non-expert users want to take control of critical-decisions, i.e. adjust the system’s autonomy. This is accomplished by interacting with users and asking for their intervention in decisions, according to their own preferences.