Systems of systems (SoS) are assemblies of systems workingtogether to achieve a common goal. Each integrated sys-tem keeps its own project management and ability to workoutside the SoS. Designing a SoS implies the ability to in-tegrate design data coming from multiple sources most ofthe time in a heterogeneous design environment, involvinga wide range of application domains, professions, method-ologies and communication means. To dene such systems,it is crucial to dene an architecture that takes in accountthe functionalities required by all the stakeholders, and toenable their simulation as a mean to provide the stakehold-ers with a global view of a SoS before deployment. In thispaper, we dene some principles that drive the develop-ment of a new functional architecture simulator in the con-text of SoS engineering. To tame the heterogeneity of SoScomponents, design tools, and methodologies, we sketch anew model-transformation approach that unies parsing andmodel transformation.