Server software in the 4300 instrument controls electrophoresis and stores data on its internal hard disk. When runs are started from e-Seq software, the 4300 takes control, starts electrophoresis, and collects image data. One computer can control multiple instruments. The computer running e-Seq is not needed during electrophoresis and can be used to perform other tasks, such as data analysis, office computing, starting runs on other instruments, etc.

Electrophoresis image data from runs are stored on the 4300's internal hard disk. When a finished run is opened with e-Seq, image data are automatically transferred to the computer and for base calling.