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Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local(More)
We present an algorithm for the layout of undirected compound graphs, relaxing restrictions of previously known algorithms in regards to topology and geometry. The algorithm is based on the traditional force-directed layout scheme with extensions to handle multi-level nesting, edges between nodes of arbitrary nesting levels, varying node sizes, and other(More)
  • O. Babur, E. Belviranli, +10 authors C. Kucukkececi
  • 2006
Although there has been an enormous amount of effort for creating ontologies, standards and tools, current bioinformatics infrastructure is far from coping with the dramatically increasing amount of biological data. The PATIKA Project aims to provide the scientific community with an integrated environment for modeling, analyzing and integrating cellular(More)
  • İlknur Kaynar, Yasemin Satıroğlu, +26 authors Sinan Uşşaklı
  • 2003
Introduction One of the most important principles in software engineering for coping with complexity and achieving quality software is the separation of concerns principle. This principle states that a given design problem involves different kinds of concerns, which should be identified and separated in different modules. The history of software development(More)
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