An electrowetting on dielectric (EWOD) device includes a first substrate assembly and a second substrate assembly spaced apart to define a channel between them; an input port in fluid communication with the channel, the input port defining an input well for receiving a fluid for inputting into the channel; and a control port in fluid communication with the channel, the control port defining a control well for receiving a fluid and having a seal that seals the control port in a sealed state in which fluid is restricted from entering the control well from the channel. When the seal is pierced, the control port is placed in an unsealed state permitting fluid to enter the control well from the channel. The electrowetting force may be manipulated to remove the dispensed droplets via an exit port. Multiple cycles of fluid input/droplet manipulation/fluid extraction may be repeated to perform complex reaction protocols.