We have developed two processes with the Biomek FX robot to construct 454 titanium and Illumina libraries in order to meet the increasing library demands. All modifications in the library construction steps were made to enable the adaptation of the entire processes to work with the 96-well plate format. The key modifications include the shearing of DNA with Covaris E210 and the enzymatic reaction cleaning and fragment size selection with SPRI beads and magnetic plate holders. The construction of 96 Titanium libraries takes about 8 hours from sheared DNA to ssDNA recovery. The processing of 96 Illumina libraries takes less time than that of the Titanium library process. Although both processes still require manual transfer of plates from robot to other work stations such as thermocyclers, these robotic processes represent about 12- to 24-folds increase of library capacity comparing to the manual processes. To enable the sequencing of many libraries in parallel, we have also developed sets of molecular barcodes for both library types. The requirements for the 454 library barcodes include 10 bases, 40-60percent GC, no consecutive same base, and no less than 3 bases difference between barcodes. We have used 96 of the resulted 270 barcodes to construct libraries and pool to test the ability of accurately assigning reads to the right samples. When allowing 1 base error occurred in the 10 base barcodes, we could assign 99.6percent of the total reads and 100percent of them were uniquely assigned. As for the Illumina barcodes, the requirements include 4 bases, balanced GC, and at least 2 bases difference between barcodes. We have begun to assess the ability to assign reads after pooling different number of libraries. We will discuss the progress and the challenges of these scale-up processes.

The project reuses the sensor and actuator interface software developed by California PATH for the DEN1097 automated highway system demonstration on Highway I17 in San Diego during August 1997. This software is provided on the QNX operating system. It interfaces with the magnetometers, radars, and the various intenal sensors such as wheel speed, engine speed, steering angle, etc, as well as with the actuators such as throttle, brake, and steering. In this project, we wrote an interface process that communicates between the driver process described above and the controller process described below. The interface process is required because the driver process works in a blocking communication mode while the controller process works in a non-blocking communication mode. The controller process is provided in three flavors: lateral control only, longitudinal cont'rol only, and integrated lateral and longitudinal cont,rol.

This thesis describes two studies aiming to enhance the speed, accuracy and practicality of the P300 Speller. The first study introduces the Inverting paradigm, which is based on the hypothesis that a modification in the visual stimulus paradigm in order to increase the stimulus saliency and strength might enhance the physiological response and hence system performance. The second study compares Speller performance using a minimal four electrode set, versus the 32 and six electrode sets previously used and described in literature. The Inverting paradigm significantly improved Speller speed and accuracy, along with an increase in the physiological response. The minimal electrode set maintained comparable levels of performance and hence increased the system practicality.