Methods and tools for visualization and management of SBGN process description maps

buir.advisorDoğrusöz, Uğur
dc.contributor.authorSarı, Mecit
dc.date.accessioned2016-01-08T20:18:16Z
dc.date.available2016-01-08T20:18:16Z
dc.date.issued2014
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 70-71.en_US
dc.description.abstractGraphs are commonly used to model relational information in many areas such as relational databases, software engineering, biological and social networks. In visualization of graphs, automatic layout, interactive editing and complexity management of crowded graphs are essential for effective utilization of underlying information. Advances in graphical user interfaces have given rise and value to interactive editing and diagramming techniques in graph visualization. As the size of the information to be visualized vastly increased, it became harder to analyze such networks, making use of relational information needed to be acquired. To overcome this problem, sophisticated and domain-specific complexity management techniques should be provided. The Systems Biology Graphical Notation (SBGN) has been developed over a number of years by biochemists and computer scientists to standardize visual representation of biochemical and cellular processes. SBGN introduces a concrete, detailed set of symbols for scientists to represent network of interactions, in a way that is not open to more than one interpretation. It also describes the manner, in which such graphical information should be interpreted. The SBGN Process Description (PD) language shows how entities are influenced by processes, which are represented by several reaction types in a biological pathway. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram. We developed methods and tools to effectively visualize and manage SBGNPD diagrams. Specifically, we introduced new algorithms for proper management of complexity of large SBGN-PD diagrams. These algorithms strive to keep SBGN-PD diagrams intact as complexity management takes places. In addition, we provided software components and web-based tools that implement these methods. These tools use state-of-the-art web technologies and libraries.en_US
dc.description.provenanceMade available in DSpace on 2016-01-08T20:18:16Z (GMT). No. of bitstreams: 1 1.pdf: 78510 bytes, checksum: d85492f20c2362aa2bcf4aad49380397 (MD5)en
dc.description.statementofresponsibilitySarı, Meciten_US
dc.embargo.release2016-08-19
dc.format.extentxv, 71 leaves, graphicsen_US
dc.identifier.itemidB133269
dc.identifier.urihttp://hdl.handle.net/11693/18322
dc.language.isoEnglishen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectBioinformaticsen_US
dc.subjectBiologyen_US
dc.subjectGraph Visualizationen_US
dc.subjectPathwaysen_US
dc.subjectSBGNen_US
dc.subjectComplexity Managementen_US
dc.subjectVisualization Softwareen_US
dc.subjectWeb-based Softwareen_US
dc.subject.lccQH324.2 .S37 2014en_US
dc.subject.lcshBiological systems--Computer simulation.en_US
dc.subject.lcshBioinformatics.en_US
dc.subject.lcshBiology--Data processing.en_US
dc.subject.lcshTechnical illustration.en_US
dc.subject.lcshScientific illustration.en_US
dc.subject.lcshInformation visualization.en_US
dc.subject.lcshComputational biology.en_US
dc.titleMethods and tools for visualization and management of SBGN process description mapsen_US
dc.typeThesisen_US
thesis.degree.disciplineComputer Engineering
thesis.degree.grantorBilkent University
thesis.degree.levelMaster's
thesis.degree.nameMS (Master of Science)

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