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Computational Biology Core

Collaborating Institution: University of Texas Southwestern Medical Center at Dallas, Dallas, TX

Director: Harold Garner

Description: There is a need for bioinformatics support at all levels and times for projects in the Regional Centers of Excellence (RCE) to maximize the efficiency and speed of the research, and to make the results of RCE research available to scientists and others to utilize those findings to advance anti-biothreat work across the nation. Bioinformatics tools, custom databases, experimental designs, data acquisition/archival/access methods and data analysis/interpretation methods are anticipated to have great impact on the progress of the RCE, and these will be the deliverables of a bioinformatics program. New bioinformatics technologies will be developed that integrate and analyze many diverse types of data. Ideas for these tools will come from the biological scientists working on the projects, but bioinformaticists will develop the solution. We will also leverage the existing commercial and non-commercial systems (tools, databases, development environments) to speed the bioinformatics solution development for maximum data exchange compatibility, and for issues like security and robustness.

The specific aims for this core are:
1) To develop applied computational biology resources (codes, databases, and interpretations of data) to facilitate advances in the understanding and characterization of Class A-C pathogens, and to provide computational support for project investigators.
2) To apply our computer codes (new and pathogen-adapted) to pre-compute a variety of data for Class A-C pathogens. This will include ORF amplification primers for PCR and qPCR, DNA chip oligonucleotide probes for re-sequencing and expression, a collection of text-based literature, and extracted and associated biomedical objects.
3) To construct a pathogen-specific, internet accessible, world wide web-based bioinformatics tool set and data warehouse of utilities that is available to facilitate intra- and inter-institutional collaborations among project personnel and others in the biothreat and emerging pathogen research community.
4) To establish and maintain computer servers to support this effort.