DBI Bioinformatics Core Center

The Bioinformatics Core Center has been incorporated into the Center for Bioinformatics & Computational Biology as of Spring 2009.  Services to the greater DBI community will continue with few, if any, changes.

The BioIT Center at the Institute houses a compute cluster, a database cluster, a visualization studio, along with multiple specialized servers.

The Visualization Studio, one of the first in the country to be dedicated primarily to life-sciences research and education, is essentially a darkened room with a 100-ft² screen, providing an interactive, immersive, 3D graphics environment for up to ten researchers and students. A pair of digital projectors that are positioned behind the 15ft x 7ft screen deliver a rear-projected, edge-blended image with a total resolution of 2240x1024 pixels. Ultrasonic sensors mounted in the ceiling of the studio track the motion of the lead researcher’s head and of a handheld 3-D wand, allowing for an experience where the team members can literally immerse themselves within the data. The display is driven by two servers. An eight-processor Silicon Graphics Prism visualization supercomputer with four graphics pipelines provides a Linux environment with the power of the SGI graphics software. A dual-core HP AMD64 with a high-end NVidia graphics processor will allow the wealth of Windows software to be utilized.

In September 2003, the BioIT Center installed a Sun Microsystems SunFire V60x Linux Compute Cluster, featuring 128 dual processor 2.8 GHz Xeon CPUs, a 48-Node Myrinet Switch, 160 Gigabyte of Memory, and over a Terabyte of disk storage. Since that time, the cluster has been upgraded to include several AMD64-based servers. Funded jointly by the NIH-BRIN/INBRE grant and the NIH-COBRE “Structural and Functional Genomics” grant, this computational capacity will allow researchers to significantly reduce processing time for CPU-intensive research related to genomics, proteomics and biophysical chemistry.

In support of the organization and analysis of the rapidly growing amount of genomic and proteomic data, a cluster of six Sun Microsystems SunFire X4200M2 systems is available as a database server. Each system has 4 AMD64 cores, 16GB memory, and 300GB local disk space. In addition, an Apple 10.5TB RAID array, a 840GB Sun RAID array, and a 480GB Sun JBOD array are available as shared storage across all servers. MySQL and Oracle database systems are available on the SunFire X4200's to organize, store and evaluate the rapidly growing amount of data, both from external databases as well from internal sources such as the microarray center, the mass spec facilities in the proteomics center, the bioimaging center and from several DNA sequencers in the DBI Network.

Complementing its computational resources, the Bioinformatics Center offers access to a variety of bioinformatics analysis tools, with state-wide licenses in place for Vector and Xpression NTI, and Sequencher as well as a broad number of publicly available sequence analysis programs. In addition, several software tools used for biomolecular modeling and visualization, including Gaussian, MOE, Amira, and Spider, have been installed at the BioIT Center to meet the needs of the biochemistry community for protein simulation and analysis.

Dr. Douglas O’Neal serves as Manager of the BioIT Center, and database support of faculty projects is provided by Dr. Mihailo Kaplarevic as Bioinformatics Associate Scientist. Desktop support is provided by Mr. Eric Garrison as Systems Administrator III.

Major funding for the BioIT Center was provided by the National Center for Research Resources of the National Institutes of Health (NIH-NCRR) under the Delaware BRIN and INBRE programs with matching funds provided by the State of Delaware.