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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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