Automated layout of process description maps drawn in systems biology graphical notation = Systems biology graphical notation kullanılarak çizilen proses diyagramlarının otomatik yerleştirilmesi

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buir.advisorDoğrusöz, Uğur
dc.contributor.authorGenç, Begüm
dc.date.accessioned2016-01-08T20:18:26Z
dc.date.available2016-01-08T20:18:26Z
dc.date.issued2014
dc.departmentDepartment of Computer Engineeringen_US
dc.descriptionAnkara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent University, 2014.en_US
dc.descriptionThesis (Master's) -- Bilkent University, 2014.en_US
dc.descriptionIncludes bibliographical references leaves 74-78.en_US
dc.description.abstractEvolving technology has increased the focus on genomics. The combination of today’s advanced studies with decades of molecular biology research yield in huge amount of pathway data. These models can be used to improve high-throughput data analysis by linking correlation to the causation, shedding light on many complex diseases. In order to prevent ambiguity and ensure regularity of the research, a need for using a standard notation has emerged. Systems Biology Graphical Notation (SBGN) is a visual language developed by a community of biochemists, modellers and computer scientists with the intention of enabling scientists to represent networks, including models of cellular processes, in a standard, unambiguous way. SBGN is formed of three languages: process, entity relationship and activity flow. This research is focused on its process diagram branch. Automated layout is commonly used to clearly visualize the information represented by graphs. Considering the fact that, biological pathways includes nested structures (e.g., nucleoplasms), we have made use of a force-directed automatic layout algorithm called Compound Spring Embedder (CoSE), which supports the compound graph structures. On top of this layout structure, we have developed a specialized layout algorithm called SBGN-PD layout. SBGN-PD layout enhancements mainly include properly tiling of complex members and disconnected molecules, placement of product and substrate edges on the opposite sides of a process node without disturbing the force-directed structure of the algorithm.en_US
dc.description.degreeM.S.en_US
dc.description.provenanceMade available in DSpace on 2016-01-08T20:18:26Z (GMT). No. of bitstreams: 1 1.pdf: 78510 bytes, checksum: d85492f20c2362aa2bcf4aad49380397 (MD5)en
dc.description.statementofresponsibilityGenç, Begümen_US
dc.embargo.release2016-08-19
dc.format.extentxiv, 78 leaves, graphicsen_US
dc.identifier.itemidB148076
dc.identifier.urihttp://hdl.handle.net/11693/18342
dc.language.isoEnglishen_US
dc.publisherBilkent Universityen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectInformation visualizationen_US
dc.subjectGraph layouten_US
dc.subjectAutomatic layouten_US
dc.subjectBiological networksen_US
dc.subjectBiological process diagramsen_US
dc.subjectGraph algorithmsen_US
dc.subjectGraph visualizationen_US
dc.subjectSystems biology graphical notationen_US
dc.subjectCompound spring embedderen_US
dc.subject.lccQ222 .G46 2014en_US
dc.subject.lcshInformation visualization.en_US
dc.subject.lcshScientific illustration.en_US
dc.subject.lcshDigital images.en_US
dc.titleAutomated layout of process description maps drawn in systems biology graphical notation = Systems biology graphical notation kullanılarak çizilen proses diyagramlarının otomatik yerleştirilmesien_US
dc.typeThesisen_US

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