This presentation describes the details and lessons learned from implementing a genomic sequencing system that integrates development, user interface, and data access for diverse applications including, but not limited to, laboratory information management systems (LIMS), quality control, sequence analysis, assembly, and annotation.
We continue to evolve the informatics infrastructure at LANL in support of genomic sequencing. We require an infrastructure that allows for quick adaptation by a small bioinformatics team in a dynamic, complex environment. In addition to constant change, our applications entail high-throughput, memory-intensive algorithms, relatively few users on diverse platforms, and lots of data. With these constraints, our challenge was to build a new infrastructure that would allow us to support current and future development while continuing to support existing Java applications. The architecture we chose to implement is a multi-tier system based on J2EE (Java 2 Enterprise Edition) with Oracle as the backend, Silverstream or Oracle 9iAS as the middle tier application server, and primarily Java applications on the client side. Our first application built on this new foundation is a decision support system for production finishing.