Improvements on pathwaymapper: a collaborative pathway curation tool

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buir.advisorDoğrusöz, Uğur
dc.contributor.authorDervishi, Leonard
dc.date.accessioned2018-07-27T08:41:16Z
dc.date.available2018-07-27T08:41:16Z
dc.date.copyright2018-07
dc.date.issued2018-07
dc.date.submitted2018-07-25
dc.descriptionCataloged from PDF version of article.en_US
dc.descriptionThesis (M.S.): Bilkent University, Department of Computer Engineering, İhsan Doğramacı Bilkent University, 2018.en_US
dc.descriptionIncludes bibliographical references (leaves 41-45).en_US
dc.description.abstractInformation visualization focuses on visually representing abstract data to amplify human cognition. Graph visualization is one of the most common types in the eld of information visualization because of its capabilities to present huge amount of data in a clear and meaningful manner. A graph is a suitable data structure for representing relational information and for this reason graph visualization has a wide usage in biological pathway visualization as well. In this thesis, we focus on collaborative construction of cancer pathways and visualization of cancer genomics data overlaid over such networks. Several biological pathway visualization tools have been developed to help biologists analyze cancer genomics data, using various formats, including standard formats like SBGN, in the past. Nevertheless, most biologists prefer curated pathway diagrams like the ones featured in The Cancer Genome Atlas (TCGA) manuscripts, using a simpler notation. These pathway diagrams outline the alterations occurring in pathways for di erent cancer types. To address this need, a web-based tool called PathwayMapper was previously developed. PathwayMapper can be used to view pre-curated cancer pathways or to create new pathways from scratch. It has many features including overlay of genomic alteration data from the cBioPortal. It also includes a collaborative mode so that the users can interactively create and modify the cancer pathways. With this thesis, we improve PathwayMapper in several ways to make it a more complete and powerful editor with a better user interface. New features include complexity management operations, edge bend support, interactive node resize, and various highlighting capabilities. Furthermore, the user interface has been improved to be more user friendly with the addition of a toolbar.en_US
dc.description.provenanceSubmitted by Betül Özen (ozen@bilkent.edu.tr) on 2018-07-27T08:41:16Z No. of bitstreams: 1 Thesis_Leonard_Dervishi.pdf: 2129250 bytes, checksum: c73a09dd4a2741e1e2808f8769a208f8 (MD5)en
dc.description.provenanceMade available in DSpace on 2018-07-27T08:41:16Z (GMT). No. of bitstreams: 1 Thesis_Leonard_Dervishi.pdf: 2129250 bytes, checksum: c73a09dd4a2741e1e2808f8769a208f8 (MD5) Previous issue date: 2018-07en
dc.description.statementofresponsibilityby Leonard Dervishi.en_US
dc.format.extentxii, 45 leaves : charts (some color) ; 30 cm.en_US
dc.identifier.itemidB158734
dc.identifier.urihttp://hdl.handle.net/11693/47683
dc.language.isoEnglishen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectGraph Visualizationen_US
dc.subjectPathway Editoren_US
dc.subjectSystems Biologyen_US
dc.subjectBiological Pathwaysen_US
dc.subjectCancer Genomicsen_US
dc.subjectPathway Curation Toolen_US
dc.subjectWeb-Based Ssoftwareen_US
dc.titleImprovements on pathwaymapper: a collaborative pathway curation toolen_US
dc.title.alternativeOrtaklaşa yolak kürasyon aracı pathwaymapper'a iyileştirmeleren_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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