Computational Science

McGlothlin-Street HallThe College of William and Mary, the Virginia Bioinformatics Institute (VBI) and the Institute for Computational Genomics (INCOGEN) recently received a $3.2 million award from the Commonwealth Technology Research Program (CTRF) to create a cooperative bioinformatics program. INCOGEN has relocated from South Carolina to the Busch Corporate Center in James City County.

INCOGEN offers bioinformatics software and services to optimize analysis and mining of genomic data. INCOGEN is a founding member of the Interoperable Informatics Infrastructure Consortium. Known as I3C, this organization consists of over 70 international leaders from major life science and information technology companies. The purpose of this organization is to develop common protocols and interoperable technologies for data exchange and knowledge management for the life science community. INCOGEN recently received a $2 million grant from the National Institute of Standards and Technology to develop new tools for genomic analysis.

The Virginia Bioinformatics Institute at Virginia Tech is an interdisciplinary research institute with both computational (60%) and laboratory facilities (40%). The laboratory facility is dedicated to the development and delivery of technologies for the large-scale discovery of biological macromolecules (DNA, mRNA, proteins and metabolites). The laboratory currently operates DNA sequencing, microarray and affymetrix gene chip technologies. The computational facility operates a 196 CPU IBM Cluster, an IBM Shark Storage Area Network with two terabytes of disk space, a SUN Enterprise 15,000 with 72 processors and a "research only" 16 node IBM SP2. VBI also has access to another 200 CPU Beowulf computer cluster.

W&M, INCOGEN and VBI will focus collaboratively on three interrelated research areas:

  • development of accurate, reliable and efficient models and algorithms for the analysis, representation, communication, and interpretation of data in the life sciences;
  • development of software that is intuitive and easy-to-use, and that hides the complexities of managing and mining huge databases across the Internet; and
  • development of experimental, computational, and theoretical aspects of molecular and cellular biology including the simulation of modeling of dynamical aspects of cell signaling. This research area will extend the interpretation and study of genomic, functional genomic (transcriptional level), proteomic, and metabolomic information to a larger scale by exploring interactions at the cellular level.

Under the CTRF grant, W&M will purchase microarray analysis and automatic gene sequencing equipment, hire a supporting technician and fund post-docs, graduate and undergraduate students. INCOGEN will help strengthen William and Mary's bioinformatics infrastructure by providing two of their software products; GenePort and VIBE. They will also establish a web-based bioinformatics training environment for students and faculty. INCOGEN will use W&M's Computer Science Cluster (SciClone) and VBI's computing resources to evaluate and demonstrate the efficacy and performance of new software frameworks that support distributed genomic analysis. W&M's SciClone is a heterogeneous computational facility consisting of over 300 processors with aggregate peak performance of 362 billion floating-point operations per second, 236 gigabytes of memory, and 15.1 terabytes of disk storage. The College and INCOGEN will seek out other computer platforms for software testing. Inquires of this nature should be directed to Dr. John Van Rosendale, Director, Computational Science Cluster at (757) 221-2003.

The department of Applied Science at W&M also offers undergraduate minors in computational biology and materials science.  In addition, W&M will create a Bioinformatics Ph.D. track within Applied Science.  Applied Science currently has approximately 50 Ph.D. students and anticipates expanding into biomaterials, imaging, and bioinformatics.