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About the
Bilkent Center for Bioinformatics
Bioinformatics is the emerging
science of managing and analyzing biological data through advanced
computing technologies. The Bilkent
Center for Bioinformatics (BCBI), based at Bilkent University in
Ankara, Turkey, is a research and development center for students
and faculty in bioinformatics. Since its founding in 2002, the
center has participated in successful research and development
projects such as VISIBIOweb and ChiBE. The results from
these projects have been published in many prestigious journals
including Nature Biotechnology, Bioinformatics, and
Proteomics.
BCBI's PATIKAweb
PATIKA, an acronym for Pathway
Analysis Tools for Integration and Knowledge Acquisition, is a
BCBI project with a goal of creating database query software. To
fulfill this goal, BCBI developed PATIKAweb,
a lightweight and powerful web-based service that allows users to
integrate, query, analyze, and manipulate biological pathways from
the PATIKA database. Researchers use
the application to rapidly acquire knowledge, interpret
microarray-generated large-scale data, identify diseased genes,
and develop drugs. It includes an integrated visual environment
with a central database that can capture all possible events
within a living cell. Users can construct and analyze cellular
pathways in an intuitive and effective manner. PATIKAweb's
user-friendly interface and visual editor enables users to
interact with and highlight critical pathways within their data
for a comprehensive analysis.
BCBI's
Challenge
Recent advancements in biotechnology
have dramatically increased the amount of biological pathway data.
Traditionally, biologists have relied on hand-drawn static
pictures of pathway maps and text-based analysis. However, they
now need a powerful and scalable tool to help them manage,
understand, and make sense of the vast amount of information. Visual representations of data would
enable biologists to conduct a more comprehensive analysis of
existing data and communicate the results. BCBI wanted their
online system to display pathway details quickly and clearly, so
they decided to include a visualization component in PATIKAweb.
According to Dr. Ugur Dogrusoz,
Director of BCBI, "Visual representations are much more
explanatory and easier to communicate with. We needed a thin
client that included dynamic visualization powerful enough to
handle the vast amount of information in our database."
Choosing Tom
Sawyer
BCBI required that their application
contains certain features, such as interactive editing, object
inspection, and complexity management. They also wanted to meet
the demands of users by providing a cross-platform product that
required minimum installation.
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Dr. Dogrusoz
remarked, "When choosing a visualization software, I was and
still am confident that Tom Sawyer Software is the only software
with the quality, reliability, and broad range of capabilities
that meets our visualization needs. Tom Sawyer Software products
are extremely reliable and excel in providing highly configurable
drawings in various layout styles. Tom Sawyer Visualization, JSP
Edition, includes the functionalities we needed. Integration was
smooth, and the Tom Sawyer team promptly addressed any questions
we had."
The Tom Sawyer
Solution
Tom Sawyer Visualization, JSP Edition,
provides flexible and extensible JSP components and Java class
libraries for adding graph visualization functionalities to web
applications quickly and efficiently. Tom Sawyer Visualization
provides the browser-based technology that BCBI needed to build an
application that does not require user installation or
registration. By incorporating Tom Sawyer Visualization’s powerful
functionalities, PATIKAweb features a user-friendly
interface, dynamic visualization, and automated layout for simple
or advanced graph-theoretic querying of the PATIKA database.
"With Tom
Sawyer Visualization, it took only a few weeks to build a
visualization component for PATIKAweb that presents and
exposes hidden relations among biological pathways. Without a
library like this, we may have spent years to get a similar visual
component, and with missing capabilities," stated Dr.
Dogrusoz.
The Tom Sawyer
Impact
The integration of Tom Sawyer
Visualization offers PATIKAweb state-of-the-art
visualization techniques that dramatically enhance its users'
research. PATIKAweb’s visualization component provides the
necessary tools to easily access, integrate, and create
sophisticated customized diagrams of pathways in an interactive
environment. With graphically rich representations and automated
layout capabilities, users can clearly see and understand the
relationships and interactions in their complex biological data. Dr. Dogrusoz said, "Our users
immediately notice the superior visualization component. Without
the ability to graphically visualize data, it is extremely
difficult to predict which pathways are important. Tom Sawyer
Software makes it a lot easier and faster to analyze underlying
pathways and experiment with data. The effective visualization
capabilities dramatically reduce the time and cost required for
research and development."
Overview
- Facilitate overlay of experiment data
onto pathways for effective analysis
- Identify critical pathways from an
exhaustive list of events within a living cell
- Model networks of cellular process,
incomplete information, and abstractions at varying levels
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