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Computational
Biology Core
Collaborating Institution: University of Texas Southwestern Medical
Center at Dallas, Dallas, TX
Director: Harold Garner, PhD
Description: Bioinformatics tools, custom databases, experimental
designs, data acquisition/ archival/ access methods, data analysis,
and data interpretation methods will continue to have great
impact on the RCE progress and will be the deliverables
of the bioinformatics
program. New bioinformatics technologies will be developed,
and they will be required to integrate and analyze the
many diverse
types of data WRCE investigators generate. Ideas for these
tools will come from the biological scientists working
in the projects
and cores as well as bioinformaticists in our core, but bioinformaticists
will develop the tools. We will leverage the existing commercial
and non-commercial systems (tools, databases, development environments)
to speed the bioinformatics solution development; for maximum
data exchange compatibility issues, such as security; and
for robustness.
In the previous grant period, we created numerous tools and
databases, which have had tens of thousands of users. We have
analyzed over
25 large array-based datasets and have reported this work in
13 publications.
The
Specific Aims for this core are:
To develop applied computational
biology resources–codes,
databases, and interpretations of data–to facilitate
advances in the understanding and characterization of Category
A-C pathogens,
to validate the performance of the codes and databases
either collaboratively or via wet lab testing, and to provide
computational
support for
project investigators.
To apply our computer codes (new and pathogen-adapted)
to pre-compute a variety of data for Category A-C pathogens,
including
ORF amplification
primers (PCR, qPCR), DNA chip oligonucleotide probes for
re-sequencing and expression, and a collection of text-based
literature and
its extracted and associated biomedical objects.
To construct a pathogen-specific, internet accessible,
www-based bioinformatics tool set and data warehouse of utilities
and
make them available to facilitate intra- and inter- institutional
collaborations
among project and core personnel and others in the biothreat
and emerging pathogen research community.
To provide an experimental design data analysis and interpretation
collaborative service to RCE researchers, especially for
data-intensive studies such as pathogen or host expression,
proteomics, or
genomics.
To continue to expand and maintain computer servers to
support this effort.
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