Laboratory Information Management Systems
The rapid growth of the BCM-HGSC has been accompanied by rapid changes in sequencing technology and applications. In the presence of sequence production operations more akin to industry than to academia, development of our production pipeline requires planning that combines skills from the fields of biotechnology, systems engineering, computer-human interface, database design, distributed computing systems, and workflow management systems. The chief requirements of the laboratory information management systems (LIMS) are sample and processing tracking for submissions and chain of custody tracking for quality control.
The nature of the LIMS in place at the BCM-HGSC has changed from early days in which the vast preponderance of output was random Sanger "shotgun" sequence generated from whole genome or bacterial artificial chromosome DNA, in which source material was uniform across an entire 96 or 384 well tray. With the arrival of medical re-sequencing, tracking precision changed to require mapping PCR primers and sample material on a well by well basis, as well as abstractions necessary to preserve anonymity of human subjects.
Second generation sequencing technologies retain these requirements for DNA materials tracking, but also pose new challenges centered chiefly around the huge volume of raw data generated, so that disk space management comes to play an increasingly significant role in processing. In addition, because these different technologies exhibit different strengths and weaknesses with respect to sequence quality, project management tools become increasingly important, as different applications may benefit from sequence production on complementary platforms.