Core Programs

Bioinformatics Core

Core Director: Michael Hauser, PhD

The Bioinformatics Core employs state-of-the-art methods to harness the resources of the Human Genome Project for the benefit of CHG researchers and collaborators. The core consists of two full-time bioinformatics programmers who fulfill the needs of individual research projects through the design and implementation of custom bioinformatics modules programming. The Bioinformatics Core also maintains a set of core applications and databases for the general use of all CHG researchers and collaborators.

Regular bioinformatics tutorials enable researchers to implement these applications and databases on their own. For example, we teach a bioinformatics “Genome Access Workshop” here at Duke, in collaboration with researchers at the Sanger Institute. This workshop covers a wide variety of techniques and approaches to using available genomics resources. It is open to the entire university and is well-attended and well -received by a wide range of individuals from both the medical center and university.

The cornerstone of the Bioinformatics Core is a local Ensembl server that displays the most up-to-date assembly of the human genomic sequence. It also displays a wide variety of genomic data such as single nucleotide polymorphisms, annotated genes and expressed sequence tags (ESTs), microarray probes, microsatellite markers, repeat sequences, and recombinationally at-risk DNA elements. In addition, this Ensembl server uses the distributed annotation system (DAS) to display locally generated genomic data (such as linkage peaks and associated markers) in the context of the fully annotated public sequence.

Resources provided by the Center for Human Genetics Bioinformatics Core include:

• A local Ensembl server using the distributed annotation system (DAS) with our own CHG-developed E-DAS software to display the current genomic sequence assembly, along with locally generated genomic data.
  
• CHG-developed Variation Database for mutation and gene variations in family/participant data.
  
• The Sunfire 12K supercomputer, administered cooperatively with Duke OIT.
  
• Ownership of several computing nodes provides access to the Linux computer cluster maintained by OIT.
  
• Custom bioinformatics programming to address the informatics needs of individual projects.
  
• Regular bioinformatics tutorials to train end-users in the use of a variety of bioinformatics tools.
  

The mission of the bioinformatics core is to provide Duke CHG faculty, staff, and collaborators with integrated bioinformatics solutions in support of human genetics and genomics research.

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