100. A Distributed Object System for Automated Processing and Tracking of Fluorescence Based DNA Sequence Data 

Michael C. Giddings, Jessica M. Severin, Michael Westphall, and Lloyd M. Smith 
University of Wisconsin, Madison, Wisconsin 
jseverin@chem.wisc.edu 

We have been developing a system which allows for rapid and easy construction of data handling and analysis for DNA sequencing through the use of modular componentware which can be assembled into a working analysis system through an easy to use graphical interface. This system utilizes network-distributed object communications for data transfer and process synchronization allowing the integration of processing programs and components located on different hardware and software platforms. Our analysis system focuses on automated processing of raw data collected on four color fluorescence based DNA sequencing instruments to the point of base calling. This system employs a distributed object framework which allows easy integration of new components into the analysis system. A new component can even be an existing analysis program available as a precompiled command-line tool such as Phred or Phrap. We currently have 5 individual component servers implemented using this frame work. These correspond to the steps of input of new gel data into the system, automatic lanetracking, manual checking of lane tracks, lane extraction into trace data, and finally lane trace preprocessing and basecalling by BaseFinder. The last element is the "System Controller" which handles setup of system, data flow, information tracking, configuration of individual processing steps, handling and recovery of server failures, and parallel distributed load balancing to facilitate the use of multiple servers of the same type distributed across multiple machines. Parallel distributed load balancing will allow the system to scale with sequence processing demands by the simple addition of more processing computers and duplicate servers.