Ayla Solomon: A GUI Problem: Designing and implementing a graphical user interface that creates finite state machines

DNA sequencing is a technology with many important implications in medicine and one that is still developing. One method currently being explored is the use of biological nanopores to capture and hold single pieces of DNA for sequencing. Though this technology is still a long way from completion, progress is being made using feedback control to capture and manipulate DNA in the nanopores.

William Dunbar’s lab uses a field-programmable gate array, a form of reprogrammable hardware, to quickly detect changes in current caused by DNA blocking the entrance of the nanopore and react to them by changing the output voltage. To implement the logic that allows this behavior, the FPGA is programmed with a finite state machine (FSM). To create the FSMs used in the experiments, a text file had to be written that was difficult for people without a programming background to understand and work with. Because of this there was a need for an intuitive, easy-to-use graphical user interface (GUI) that would make it possible for everyone in the lab to create the FSMs required for their experiments. The GUI made this summer is just that. One grad student has already started testing and using it and hopefully it will be put to wider use in the near future.