Program Director/Principal Investigator (Last, First, Middle):
RESOURCES
University of Delaware
Center for Bioinformatics and Computational Biology (CBCB)
Bioinformatics Core Facility
Laboratory: NA
Clinical: NA
Animal: NA
Computer: The mission of the CBCB Core Facility is to provide scientific expertise and core infrastructure support in Bioinformatics and Computational Biology for the Delaware research and education community. The
CBCB is under the direction of Dr. Cathy Wu, and the activities of the Bioinformatics Core are coordinated by
Dr. Shawn Polson. Drawing on the combined resources of the CBCB, the Delaware Biotechnology Institute
(DBI), and the Protein Information Resource (PIR), the Core provides both computing infrastructure and knowledgeable personnel with significant hardware, software and professional support for bioinformatics and computational needs. Four Research Faculty with broad expertise encompassing various areas of bioinformatics analysis provide both bioinformatics/computational services and/or research collaborations. The core staff also includes a Network and Information Systems Manager and a full-time IT associate.
A special focus of the Bioinformatics Core has been the expansion of next generation sequencing
(NGS) analysis pipelines available as fee-for-service to support the growing number of investigators utilizing the advanced NGS capabilities of UD’s Genotyping and Sequencing Facility for genomic and transcriptomicbased discovery. The facility also has substantial capabilities built upon its close relationship with the Protein
Information Resource (PIR) that have been successfully applied to a number of research projects including proteomic analysis using tools such as iProExpress and literature and data mining capabilities of iProLINK.
These combined omic analysis and data integration pipelines form the nucleus of a broader bioinformatics framework that CBCB is actively developing to provide a user portal for dynamic analysis and visualization of genomic, transcriptomic, and proteomic data to its users at UD.
The Center’s in-house High-Performance Computational hardware includes over 500 processor cores supporting bioinformatic analysis. Included are approximately 200 cores freely accessible by researchers as part of our Linux-based Torque PBS cluster, BioHen. A combination of system types allows the choice of systems best suited for the particular needs of a given analysis. Included are numerous nodes configured for memory intensive computing applications with 128 - 512GB of RAM per machine. The data center currently hosts in excess of 100 TB of usable disk space. The CBCB also is a stakeholder in a campus-wide computer cluster, which will come online in fall of 2011 providing access to an additional 5000 processor cores. CLC
Genomics Workbench, JMP, JMP genomics, Matlab, and a suite of other commercial and open source
Bioinformatic and Statistical Software packages are supported and maintained on Center hardware. Our
Database Cluster is composed of 6 Sunfire X4100M2 servers and acts 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. Data security is a high priority and access to results other than through these methods is strictly limited. Our 3-D Visualization Studio is an immersive 3D graphics room with a 7'x15' rear-projection screen, delivering rear-projected, edge-blended images with total resolution of 2240 x
1024 pixels. Other resources and services include secure FTP server, file servers, on and off-site data backup servers, email server, streaming video server, web hosting, cloud-based storage interface, large format printing, administration of researcher-owned servers, and bioinformatics software license support.
Office: The CBCB has a 2500 ft 2 office and computational space located at the Delaware Biotechnology
Institute. The office suite includes space for the bioinformatics personnel on this project, including Drs. Cathy
Wu and Shawn Polson, as well as space for center researchers, graduate students, visiting faculty, and a conference room for group meetings.
Other:
PHS 398 (Rev. 6/09) Page Resources Format Page