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. The method includes the steps of making electrical measurements on the capillaries during the electrophoresis run and displaying the measurements on a display screen.