This paper reports our practical experience of benchmarking a complex System Biology Web Service, and investigates the instability of its behaviour and the delays induced by the communication medium. We present the results of our statistical data analysis and the distributions, describing the response time instability typical of Service-Oriented Architectures (SOAs) built over the Internet. We believe that performance uncertainty can be reduced by further optimisation of the internal structure and the right choice of components and technologies that suit each other and fit the system requirements better. Keywords: Web Service, Service-Oriented Architecture, Response Time, Instability.
