Using a framing protocol, an application specific integrated circuit (ASIC) in an emulation system may transmit a start-of-packet molecule to a serializer-deserializer (SerDes) interface of a switching ASIC in a gap cycle leading up to an emulation cycle such that the switching ASIC may start routing mission data through the SerDes interface during the emulation cycle. The ASIC may transmit an end-of-packet molecule at a first gap cycle to the SerDes interface of the switching ASIC such that the switching ASIC may stop routing data through the SerDes interface during the gap cycles. The start-of-packet molecule may include a start-of-packet word, a status word, cyclic redundancy check word, and an idle word. The end-of-packet molecule may include an end-of-packet word, a status word, a cyclic redundancy check word, and an idle word.