Siper, Metin Can2017-08-022017-08-022017-072017-072017-08-01http://hdl.handle.net/11693/33522Cataloged from PDF version of article.Thesis (M.S.): Bilkent University, Department of Computer Engineering, İhsan Doğramacı Bilkent University, 2017.Includes bibliographical references (leaves 61-68).Information 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.xiii, 68 leaves : charts (some color) ; 29 cmEnglishinfo:eu-repo/semantics/openAccessBiological mapsPathwaysInformation visualizationWeb based toolsSystems biologyPathway layoutComplexity managementPathway viewerPathway editorPathway curatorSBGNThesisB156071