Most of this information is taken from http://fab.cba.mit.edu/classes/MIT/863.07/10.15/ and is available there in a more concise form (minus the pictures and commentary).

Step 1:

Create an external power supply for the board, using the 4-pin AMP connector that would normally go straight to the DB-9 serial connector. This isn't really a necessary part of the USB conversion, but it is convenient, allowing us to program the board with just one connection to the computer (instead of having a connection for power in addition to the connection for programming). Since all of the boards described on this website already have a voltage limiter, it is sufficient to just directly hook up a 9-volt battery. Many of these boards do not have a mechanism to protect against reverse polarity, so be sure to hook up the cable correctly. The correct pins for power and ground are labeled on all of the hello-world series of boards.

Step 2:
Create a cable to connect from the 4-pin AMP connector to a DB-9 female serial connector. The appropriate pin combination is shown here (careful while reading this diagram... the wires in a ribbon cable are not numbered. All the numbers refer to pins on one or the other of the connectors. If you do it right, this particular cable does not require any wires to cross over each other):

serial AMP MTA plug <-> DB9F cable (wire side view):

      Tx GND
   |  2   1 |
    3   4
    Rx DTR

   plug      3   2   4   1
        DCD  Rx  Tx DTR GND
          DSR RTS CTS  RI
   DB9   1   2   3   4   5
   DB9     6   7   8   9
  

Step 3:

Create a cable that directly connects one 5-pin AMP connector to another. Both connectors should be oriented in the same direction (notice in the picture, if you look at the connectors with the space for the MTA tab towards the top of the page, the white wire is on the right side for both).

Step 4:

Create a connector from a 5-pin AMP to a DB-9 female. This will be our programming cable. The appropriate wiring diagram is:

in-circuit programming AMP MTA plug <-> DB9F 
serial (dasa) cable (wire side view):

                  ^
                  | cable direction
         3        5         8
   | MOSI (3)  GND (2)  MISO (1) |
      -RESET (4)  SCK (5)
            7        4

   plug         4 3 1 5   2        
         DCD  Rx  Tx DTR GND
           DSR RTS CTS  RI
   DB9    1   2   3   4   5
   DB9      6   7   8   9		  

		  

Step 5:

Create a board that will act as a serial programming voltage limiter. The cad.py specification is here

Step 6:

Get a USB to DB-9 male converter cable

Step 7:

Program your microcontroller. In the photo here, we are using the battery as an external power supply (connected to the 4-pin AMP/MTA connector) and programming using serial over USB. If using avrdude, you need to tell the program which port to use (-P /dev/ttyUSB0), as well as what type of connection you have (-c dasa):

avrdude -p t45 -P /dev/ttyUSB0 
        -c dasa -U flash:w:file.hex 

Step 8:

Send data to the computer. In the photo here, our board has a microphone picking up audio signals, and is sending the data to the USB port on the laptop computer.