A. Center for Bioinformatics and Computational Biology
The Center for Bioinformatics and Computational Biology (CBCB) has a 2500 ft 2 office
and computational space located at the DBI. The office suite includes space for the
bioinformatics faculty and other personnel, as well as space for graduate students,
visiting faculty, and a conference room for group meetings.
CBCB Bioinformatics Core Facility
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 transcriptomic-based 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 iProXpress 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.