Lets start with your basicEphys configuration.
In this section we will use the stimulator and the acquirer. The hardware has been configured in your startEphus file (review startEphus).
Notice that the acquirer has no pulses associated with it. It only acquires data. Our startEphus file configured a channel called 'photodiode1'.
The stimulator on the other hand only puts out data. It needs to be linked with the pulse directory (File\Open\ etc).