BioIT World

Gene Browser with a Google Feel

*By Laurie Wiegler*

*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.

As a highly visual and searchable genome browser with zoomable user

interface, Genome Projector contains four “maps:” Genome Map, Plasmid
Map, DNA Walk, and Pathway Map. Each map indicates genes in various
colors, such as rRNA in red stripes and tRNA in green stripes in the
Genome Map.

Genome Projector currently lists some 320 circular bacterial genomes,

reflecting Arakawa’s research interests, but may be expanded to include
eukaryotes.

Design was important to Arakawa. He’s a fan of Apple software because it

traditionally sports an intuitive user interface. “This is often not the
case for bioinformatics software and databases,” he says. “[I] borrowed
color schemes and layout [from iTunes],” Arakawa says, adding that he
was also inspired by Google Maps, from which he plucked its free API for
the project design.

His inspiration, however, was a Roche biochemical pathways chart. As an

undergraduate, he was fascinated by the metabolism wallchart. It seemed
to him “the grand sum of the history of biochemistry,” he recalls. He
“almost trembled with excitement to start afresh in systems biology, to
build dynamic cellular simulations on top of this knowledge.”

The result of that fervor is Genome Projector. The G-language-powered

database browser uses a Restauro-G back end to annotate the genome by
similarity searches using the BLAST-Like Alignment Tool, connecting with
protein databases such as UniProt Knowledgebase and NCBI nr. The front
end boasts Web 2.0 technologies such as AJAX and EXT 2.0 framework.

*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.”

Stein says features need to be added to Genome Projector to broaden its

appeal, such as a way to allow for annotation, so “community members can
upload data sets to visualize... the genome background,” and a way to
show more detail as one zooms in, via semantic zooming. While, “it does
have popup windows with additional information on genes and enzymes… the
lack of semantic zooming is still a big usability problem, in my
opinion,” says Stein.

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.

“From an information/visualization point of view, it is extremely

compelling; it’s very, very intuitive and it satisfies a lot of the
requirements of a good data visualization approach,” she says. However,
she is “less certain” that for researchers doing genomic analysis, “this
tool would give them the flexibility they need to zoom in on their
particular question.

*Mapping the Next Steps

*Genome Projector is slated to go beyond beta by the end of the year,
after publication, but Arakawa is already busy with plans for its next
phase.

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.”

Moreover, he would like to make it easier for Genome Projector users to

put their own pins and annotations on the maps, to allow sharing of
information, ideally with a DAS (Distributed Annotation System) backend.

Genome Projector’s future may include a resemblance to the “My Maps”

feature of Google Maps.

*Sidebar: ECell 3D*

Arakawa debuted ECell 3D at a packed house at an Intelligent Systems in
Molecular Biology conference workshop last July in Vienna. Like Genome
Projector, ECell 3D is a bioinformatics tool with a focus on ease of use.

“In my experience, [the] modeling process is mostly heuristic, with

numerous trials and errors to get the model to work right, to
sufficiently capture the cellular behavior that a scientist wants to
test and learn,” says Arakawa. Therefore, good user interface and design
that supports this process, such as ECell 3D for simulation results, and
Genome Projector for data mining and searching, are essential.”

ECell 3D boasts an interface that enables researchers to model cellular

systems in 3-D graphics. The resulting platform, controlled by
Bluetooth, is strikingly visual, looking much like a flight pattern or
constellation map.

Arakawa hopes to start integrating the software tools he’s developed so

far to create a prototype modeling environment around ECell and hopes to
achieve a “sophisticated environment” for modeling in systems biology.

“There are a number of cell simulators already available,” says Arakawa,

but he believes “Automation through knowledge integration for modeling
is a key step for the success of systems biology.” -- L.W.

________________________________________________

This article appeared in Bio-IT World Magazine.

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