This??PhD work aims at proposing a methodology and tools for the evaluation of transport protocols in the context of large scale computing environment based on high speed networks. The goal is to define and validate a benchmark for comparing different transport and congestion control approaches. Our contribution concerns??the definition of metrics, scenarios, experiments and pilot demonstrations for high demanding distributed applications. After stating the problem of evaluating transport protocols in high speed networks, we present existing methodologies for this purpose. We introduce our proposal of a tool to help users performing network experiments. We illustrate our approach with a few examples of results obtained from experiments in our Grid'5000 testbed which complements other existing approaches.