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Date of Conference: 25-29 June 2005 Conference name: Thirteenth International Conference on Intelligent Systems for Molecular Biology, ISMB 2005 PATIKAweb provides a Web service for retrieving and analyzing biological pathways in PATIKA database, which currently contains data integrated from popular public pathway databases like Reactome. It features a user-friendly interface, dynamic visualization, advanced graph-theoretic queries for extracting biologically important phenomena and exporting facilities to various exchange formats.

Date of Conference: 31 July - 4 August 2004 Conference name: Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004 The PATIKA Project aims for an informatics infrastructure to cope with the inherently complex cellular pathway data and provides software tools with sophisticated visualization technology around a central database using an extensive ontology and data integration mechanisms. It also features advanced database querying, microarray data analysis, and automatic layout components.

Cataloged from PDF version of article. Graph layout is an important problem in information visualization. All datadriven graph-based information visualization systems require some sort of an automatic geometry generation mechanism, as it is generally not directly available from the data being modeled. This is why graph layout problem has been studied extensively. However, for the case of compound graphs, there are still important gaps in this area. We present a new, elegant algorithm for undirected compound graph layout. The algorithm is based on the traditional force-directed layout scheme with extensions to handle nesting, varying node sizes, and possibly other application-specific constraints. Experimental results show that the execution time and quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory. The algorithm has also been successfully implemented as part of a pathway integration and analysis toolkit named Patika for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to represent molecular complexes and various types of pathway abstractions. Giral, Erhan M.S.

Cataloged from PDF version of article. 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 possible application-specific constraints. Experimental results show that the execution time and quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory. The algorithm has also been successfully implemented as part of a pathway integration and analysis toolkit named PATIKA, for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to represent molecular complexes and various types of pathway abstractions. (C) 2008 Elsevier Inc. All rights reserved.