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*March 1, 2008* | Following the launch last year of ECell 3D, Kazaharu
Arakawa of Keio University in Japan has launched another colorful and
intuitive bioinformatics tool. Drawing inspiration from iTunes and
Google Maps, the database browser, called Genome Projector
(www.g-language.org/GenomeProjector/
<http://www.g-language.org/GenomeProjector/>), was developed at Keio’s
Institute for Advanced Biosciences over the past year.
*Distinguishing Itself
*Genome Projector resembles Cold Spring Harbor researcher Lincoln
Stein’s GBrowse, although the two browsers do differ. For example,
Arakawa says browsers such as GBrowse are designed to be scalable
interfaces but require several user interactions, and are not genuinely
zoomable user interface (ZUI) applications.
Stein told /Bio•IT/ /World:/ “That is absolutely correct! However, there
is a trade off between speed and functionality, and the popular browsers
— I’m including Ensembl and UCSC genome browser in this — provide more
functionality at the moment.”
Arakawa says his primary aim was to “allow quick, continuous zooming as
opposed to the original KEGG [Kyoto Encyclopedia of Genes and Genomes]
Pathway and GBrowse, [which both] require page transition[s] for zooming
in and out.” But he concedes that if his team implements a human map for
Genome Projector, “it is critical to consider using semantic continuous
zooming.”
Other critics charge that Genome Projector may not be viable for
large-scale genomic analysis. Accelrys’ Nancy Latimer, product manager
for the Gene Expression, R-Statistics, and Text Analysis collections for
the company’s SciTegic Pipeline Pilot products, is doubtful.
He hopes to introduce more views, starting with KEGG Atlas. “Right now,
the only way to map certain information over the four views is by
creating a new overlay, which is computationally heavy [and takes]
several minutes to generate,” Arakawa says. “I would like to optimize
this process so that we can start providing a web service for data
mapping, and to develop a new means based only on client-side Javascript
so that it is faster with no load on the server.”
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