A layout algorithm for undirected compound graphs

buir.contributor.authorDoğrusöz, Uğur
buir.contributor.authorGiral, Erhan
buir.contributor.authorÇetintaş, Ahmet
buir.contributor.authorCivril, Ali
buir.contributor.authorDemir, Emek
dc.citation.epage994en_US
dc.citation.issueNumber7en_US
dc.citation.spage980en_US
dc.citation.volumeNumber179en_US
dc.contributor.authorDoğrusöz, Uğuren_US
dc.contributor.authorGiral, Erhanen_US
dc.contributor.authorÇetintaş, Ahmeten_US
dc.contributor.authorCivril, Alien_US
dc.contributor.authorDemir, Emeken_US
dc.date.accessioned2016-02-08T10:04:55Z
dc.date.available2016-02-08T10:04:55Z
dc.date.issued2009-03-15en_US
dc.departmentDepartment of Computer Engineeringen_US
dc.departmentBilkent Center for Bioinformatics (BCBI)
dc.description.abstractWe 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. © 2008 Elsevier Inc. All rights reserved.en_US
dc.identifier.doi10.1016/j.ins.2008.11.017en_US
dc.identifier.eissn1872-6291
dc.identifier.issn0020-0255
dc.identifier.urihttp://hdl.handle.net/11693/22804
dc.language.isoEnglishen_US
dc.publisherElsevieren_US
dc.relation.isversionofhttp://dx.doi.org/10.1016/j.ins.2008.11.017en_US
dc.source.titleInformation Sciencesen_US
dc.subjectBioinformaticsen_US
dc.subjectCompound graphsen_US
dc.subjectForce-directed graph layouten_US
dc.subjectGraph drawingen_US
dc.subjectInformation visualizationen_US
dc.subjectInformation analysisen_US
dc.subjectInformation systemsen_US
dc.subjectPhotocopyingen_US
dc.subjectVisualizationen_US
dc.subjectApplication specificsen_US
dc.subjectArbitrary nestingen_US
dc.subjectBiological pathwaysen_US
dc.subjectExecution timesen_US
dc.subjectLayout algorithmsen_US
dc.subjectLayout schemesen_US
dc.subjectMolecular complexesen_US
dc.subjectPathway integrationsen_US
dc.subjectGraph theoryen_US
dc.titleA layout algorithm for undirected compound graphsen_US
dc.typeArticleen_US

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