Libraries and tools for viewing and editing biological maps in SBGN

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buir.advisorDoğrusöz, Uğur
dc.contributor.authorSiper, Metin Can
dc.date.accessioned2017-08-02T09:45:52Z
dc.date.available2017-08-02T09:45:52Z
dc.date.copyright2017-07
dc.date.issued2017-07
dc.date.submitted2017-08-01
dc.departmentDepartment of Computer Engineeringen_US
dc.descriptionCataloged from PDF version of article.en_US
dc.descriptionThesis (M.S.): Bilkent University, Department of Computer Engineering, İhsan Doğramacı Bilkent University, 2017.en_US
dc.descriptionIncludes bibliographical references (leaves 61-68).en_US
dc.description.abstractInformation about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats including Systems Biology Graphical Notation (SBGN). E ective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewing and editing tools that support these platforms and other use cases. We propose to develop a modular software architecture to meet this need. This proposed architecture includes reusable web based libraries and easily customizable and embeddable tools developed using these libraries. Our libraries include SBGNViz.js, a Cytoscape.js based library providing a renderer and an API to develop tools visualizing pathway models represented by SBGN Diagrams, and ChiSE.js, an SBGNViz.js based library to visualize and construct pathway models represented in SBGN Diagrams, and miscellaneous Cytoscape.js extensions. Our tools are built using these libraries and include SBGNViz Viewer and Newt, which are sample applications for SBGNViz.js and ChiSE.js, respectively. Newt is being developed to become a rst web based, open source SBGN editor with full support for compound structures such as molecular complexes and compartment, advanced diagramming facilities including grid and alignment guidelines, static and incremental layout, and complexity management of large maps.en_US
dc.description.degreeM.S.en_US
dc.description.statementofresponsibilityby Metin Can Siper.en_US
dc.format.extentxiii, 68 leaves : charts (some color) ; 29 cmen_US
dc.identifier.itemidB156071
dc.identifier.urihttp://hdl.handle.net/11693/33522
dc.language.isoEnglishen_US
dc.publisherBilkent Universityen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectBiological mapsen_US
dc.subjectPathwaysen_US
dc.subjectInformation visualizationen_US
dc.subjectWeb based toolsen_US
dc.subjectSystems biologyen_US
dc.subjectPathway layouten_US
dc.subjectComplexity managementen_US
dc.subjectPathway vieweren_US
dc.subjectPathway editoren_US
dc.subjectPathway curatoren_US
dc.subjectSBGNen_US
dc.titleLibraries and tools for viewing and editing biological maps in SBGNen_US
dc.title.alternativeSBGN ile biyolojik haritanın gösterimi ve düzenlenmesi için kütüphane ve araçlaren_US
dc.typeThesisen_US
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