Abstract: An automated parallel electrophoresis system including a plurality of capillaries configured to accommodate samples during an electrophoresis run which includes a plurality of phases. The system also includes a control circuit coupled to the capillaries and configured to perform one of monitoring and regulating the capillaries, a display monitor and a computer processor coupled to the control circuit and the display monitor. The computer processor includes a input/output (I/O) interface configured to communicate with the control circuit and a first computer memory storing a display program which displays a graphical user interface on the display monitor. In addition, a method of monitoring and regulating an electrophoresis run performed on a parallel capillary electrophoresis system which comprises a plurality of capillaries configured to accommodate samples during an electrophoresis run.