The Computational Biology and Bioinformatics Laboratory (CBBL) is housed in the new IMIL facilities at the Medical Research Building in Temple. The physical resource available at this location is a 112-core Nehalem Processor Mac cluster with approximately 12 TB of storage space. Nodes in this cluster are physically linked by high-speed ethernet, and Sun Grid Engine is used as the job queueing system. The EMBOSS suite of bioinformatics tools are installed on the cluster, and are available through a web interface provided by BioTeam’s iNquiry software. However, appropriate and effective use of this resource requires a high level of comfort with command line applications and some familiarity with clustered computing environments. Access to this resource can be arranged by contacting Dr. Vincent VanBuren. VanBuren serves as the director of the CBBL and conducts independent research in the field of computational systems biology.

Current projects running in the CBBL:

  1. Bayesian Network Inference from Microarray Data. Dr. Vincent VanBuren is leveraging selected microarray data in an effort to infer causal regulatory networks from expression data on a large scale. Software: MySQL, BNFinder, and custom-built software.
  2. Identifying Ontology Enrichment Parameters by Empirical Samplin Gene Ontology enrichment tests are applied to provide provisional annotation to groups of genes identified in some high-throughput experiment, or to a list of genes constructed by some arbitrary method. However, corrections for multiple testing complicates this type of analysis. VanBuren is developing a method that uses empirical sampling to collapse multiple tests into a single statistical test, thus eliminating the need for a test correction. Software: MySQL and custom-built software.

Computational Biology and Bioinformatics Laboratory Cluster