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 Vincent VanBuren, Ph.D., F.A.H.A. at firstname.lastname@example.org. Dr. 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:
- Bayesian Network Inference from Microarray Data. Dr. 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.
- 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. Dr. 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.