Browsing by Subject "cellular pathways"

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    A framework for management of multiple views of cellular pathway graphs
    (2003) Güleşir, Gürcan
    The enhancements in genomic studies have given birth to the necessity of advanced techniques for storing, integrating and analyzing the accumulated data regarding molecular level cellular processes. Since this data is huge and complex, advanced visualization and complexity management techniques need to be developed to improve its understandability. In this thesis, we present a single subject - multiple view framework for manipulating complex pathway data, which is in the form of a directed graph. The framework facilitates visualization of potentially huge pathway data in possibly varying forms and sizes. While maintaining the subject data (i.e., pathway graph) and its views, the presented framework coordinates all the views using an observer software pattern. It ensures the validity and consistency of subject data across all views. Support for replication of biological data, which is desired to reduce complexity (i.e., high degree ubique pathway objects), is another benefit of our framework. Being a neatly modularized, isolated component of a functional pathway editor, this framework is distinguished from any other single subject - multiple view graph editing environment by addressing the domain specific needs of pathway informatics.
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    Modeling cellular processes with PATİKA
    (2001) Demir, Emek
    Availability of the sequences of entire genomes shifts the scientific curiosity toward the identification of function of the genomes in large scale as in genome studies. In the near future data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. We define an ontology for a comprehensive representation of cellular events. The model presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporations of the stored data, as well as multiple levels of abstraction. Based on this model, we present an integrated environment named PATIKA (Pathway Analysis Tool for Integration and Knowledge Acquisition). PATIKA is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that PATIKA will be a valuable tool for rapid knowledge acquisition; micro array generated large-scale data interpretation; disease gene identification and drug development