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A binary protocol is a protocol which is intended to be read by a machine rather than a human being, as opposed to a plain text protocol such as IRC, SMTP, or HTTP. Binary protocols have the advantage of terseness, which translates into speed of transmission and interpretation.
Binary protocol is also used in the context of a protocol between exactly two parties, in contrast to a multi-party protocol. Binary protocol, or binary collaboration have been used in the terminology of standards such as EbXML and EDOC. An interface in UML  may also be considered a binary protocol.