The notion of agent has of late become popular in the Grid community, as exemplified by several workshops on the use of agents in the Grid. What are agents for the Grid? What is the difference between agents and Web-services? These are questions that we address by describing a port of the SoFAR agent framework to Web services in the context of a bioinformatics Grid. In this first paper, we focus our discussion solely on issues at the transport layer. Through an agent communication language (ACL) and an abstract communication model, we have been able to define a generic API to communications, and are able to support multiple protocols, including the XML protocol, the transport mechanism of Web services. This approach facilitates the development of applications, makes our environment future-proof, and promotes the open-ness of our Grid architecture to third-party developers.