Center Overview

The Bioinformatics Core Center provides computational and consulting resources for researchers and students in Delaware. As part of the Delaware Biotechnology Institute and hosted by the University of Delaware, the center supports the computational and data management needs of the DBI research community. Services offered by the center include:

• Database and System Administration
• Computational Processing
• Data Storage/Retrieval, Analysis, and Visualization
• Web Site Design and Hosting
• 3-D Data Visualization

Services offered by the center are anchored by four major systems:

• High-Performance Compute Cluster

  The core of DBI’s HPC offering is a linux-based beowulf cluster with 121 compute nodes providing 302 computer cores. A mix of system types allows the choice of systems best suited for the particular of the computation. The nodes include:

  113 x Sunfire V60x dual-processor 2.8GHz Xeons (32-bit)/2GB memory
  7 x Sunfire X4100M2 quad-core Opterons (64-bit)/8GB memory
  1 x Sunfire X4600M2 16-core Opterons (64-bit)/128GB memory
  2 x Sunfire X4440 16-core Opterons (64-bit)/64GB memory

  All compute nodes are connected via gigabit ethernet and have access to a 5TB shared storage. A parallel Myrinet network connects 48 of the nodes allowing low-latency data transfers.

  The HPC cluster is commonly used for protein sequence alignment (NCBI Blast, EMBOSS) and molecular modeling (Gaussian, GAMESS), but also supports other bioinformatics applications as well as custom applications suited for parallel processing. Fair-use scheduling of resources is provided by the Sun Grid Engine queue management system.

• Database Server Cluster

  The Bioinformatics Center uses a cluster of six Sunfire X4100M2 servers, each with quad-processor 64-bit Opteron CPUs and 16GB memory, as a repository of experimental data in relational databases. Both MySQL and Oracle database systems are available, allowing researchers to organize, store, and evaluate their data. An Apple 10.5TB RAID array, a Sun 840GB RAID array, and a Sun 480GB JBOD array provide ample storage space for current data. An additional system, a 16-processor 64-bit Opteron with 64GB memory, is used for processing and storing data from the Illumnia Next Gen Sequencer based at DBI.

  While direct access to stored data via command line and web-based clients is provided, general access to share results is usually though customized web pages. Data security is a high priority and access to results other than though these methods is strictly limited.

• 3-D Visualization Studio

  The Visualization Studio is an immersive 3D graphics room with a 7’x15′ rear-projection screen, delivering a rear-projected, edge-blended image with total resolution of 2240 x 1024 pixels. The display is driven by two servers; an eight-processor Silicon Graphics Prism visualization supercomputer with four graphics pipelines provides a Linux environments with the power of the SGI graphics software, and a dual-core HP AMD 64 with a high-end NVidia graphics processor allows a variety of Windows software to be utilized. An integrated tracking system allows the graphics software to follow the motion of a researcher and adjust the display so that the researcher can walk around or through 3D objects. Both systems are available for molecular and biological modeling projects.

• Coffee Cluster

  The Coffee cluster’s (Latte, Americano, Mocha, and Espresso), a Dell C6100 houses the four servers. Each server contains:

  • 16-core Intel Processors running at 2.8 GHz
  • 48 GB RAM

The Bioinformatics Center also supports multiple special-purpose servers. Among these are web servers, a secure ftp server for data transfer, streaming video servers, and an email server. The Bioinformatics Core staff will work with researchers to design and purchase servers dedicated to specific groups or projects. These systems can be physically located in the Bioinformatics computer room and managed by the center’s staff if desired.

Most of the servers located at the Center have very generic names.

All data on the Center’s servers are backed up daily to a paired set of Sunfire X4500 servers, each with 24TB of disk space. One server is located at DBI while the other is in the Chapel Street data center. Server backups are kept for approximately six months, providing for both data safety and disaster recovery.