The MAS system uses a computer to store and send virtual masks to the DMD, as well as to synchronize the display and illumination of these virtual masks with the chemical steps. The virtual masks themselves are one-bit bitmaps (black and white) matching the size of the DMD. The same computer is also used to edit and send to the Expedite 8909 the sequence and protocol files needed for any given synthesis design. These files contain all the necessary instructions needed to perform the desired chemical synthesis (vide infra). The computer also receives signals from the Expedite that trigger the display of each virtual mask and its illumination via the UV LED. The first step to initiate a synthesis is sending the desired sequence (.seq) and protocol (.pro) files to the Expedite. The scheme for computer control of the synthesis is outlined in Figure . A typical sequence file will have the form of the supersequence ssTTTTTACGTACGTACGT…, with the symbol "s" representing a cleaning cycle, but any other supersequence may be used to increase synthesis efficiency . The symbols A, C, G and T would generally be used to represent the chemical cycles needed to synthesize the corresponding DNA nucleobases, instructing the Expedite to carry out a preprogrammed set of fluidics instructions contained in the protocol file. Other symbols can also be used to represent alternative user-defined protocols, such as increased/decreased photoexposures, the use of a sulfurization reagent to create a phosphorothioate linkage, or the use of other nucleic acid monomers. Once the sequence and protocol files have been received by the Expedite, the MAS 2.0 control program is opened and a project folder containing the virtual mask files is selected. After the start button is pressed, the first virtual mask is displayed in a preview pane. Now the program will wait for a trigger signal from the Expedite. The first trigger signal results in the display of the virtual mask on the DMD and in the delivery of current from the constant current power supply to the UV LED. A second trigger signal from the Expedite results in the deletion of the virtual mask from the DMD and the UV source turning off. This pattern of on and off triggers continues until the end of the synthesis, with virtual masks displayed according to their alphabetical and numerical order. Optionally, the MAS 2.0 control program can be provided with an ordered list of virtual masks to follow. The MAS 2.0 control software also generates a log file to facilitate hardware and software diagnosis. The log file includes timestamps for relevant events, including arrival of the trigger signals for the Expedite, the display of virtual masks and the generation of the TTL signals to turn the UV LED on and off. The log file also maintains a record of the room temperature and humidity. Source code for the software, as well as additional detail on its use, is available in the supplementary material.