Andrew Warren (firstname.lastname@example.org)
Timothy Driscoll (email@example.com)
Visual exploration of global metrics for prokaryotic replicons.
Next-generation sequencing methods have led to a
dramatic increase in the available number of fully sequenced prokaryotic
genomes, a trend that is sure to increase into the near future. Standard
methods for comparing multiple genomes are classically linear, and focus on
individual genes (or, at best, small handfuls of related genes). In
contrast, there is much information to be learned from a system level genome
comparison. Fortunately, there exist a number of useful metrics for
describing genomes, including gene density, GC content, promoter density, and
We propose to build a discovery-based software tool that
allows researchers to visualize a novel genome sequence relative to a
landscape of existing genomes. The core of this tool will be a 3D plot
of three metrics, chosen by the user, with a fourth metric plotted as color on
the landscape surface. Initially, our landscape will consist of all
sequenced genomes from the National Center for Biotechnology Information
(NCBI), the central clearinghouse for genomic data. In addition, users
will also be able to import their own dataset to serve as the landscape.
While we will focus on genomic data for this project, we propose to
build this tool to allow visualization of any related dataset.
The objectives of this class project will be:
Design a graphical method for the exploration
of metrics which characterize prokaryotic replicons (distinct units of a
Discover dependencies among different
metric values, even when the dependency is hidden.
Find or create global metrics that
characterize prokaryotic genomes and can be used to compare multiple
genomes. Possible sources include:
Determine the best implementation language
and graphical libraries to use for the visualization; for example:
Create a proof-of-concept tool based around a
simple user interface that features:
Provide insight into how a replicon of
interest relates to the existing "prokaryotic landscape."
an interactive 3D landscape (where each replicon is represented by a
the ability to handle an arbitrary number of metrics.
the ability to select and visually emphasize a replicon or replicons of
the ability to customize arrangement and display of metrics within the
tooltip exploration with dynamic, coordinated, statistical
representations for each metric not in the landscape.
statistics calculated with respect to all points within the tooltip
variable tooltip size.
optional: a plug-in architecture for allowing extensibility
for specific functionality (for example, automatic calculation of values
from genomic sequence files).
Both investigators have similar backgrounds, and work in
the same bioinformatics field. As a result, many of the tasks will be
handled jointly. This includes discovery and choice of metrics, data
formatting and import, and user interface design and implementation.
The investigators will be working in conjunction with
researchers at Virginia Bioinformatics Institute, and 454 Life Sciences.
Both of these groups have expressed a strong interest in developing
more sophisticated visual tools for genome comparison, and may use this
project as a template for expanded development.