• About
  • Policies
  • What is open access
  • Library
  • Contact
Advanced search
      View Item 
      •   BUIR Home
      • University Library
      • Bilkent Theses
      • Theses - Department of Computer Engineering
      • Dept. of Computer Engineering - Master's degree
      • View Item
      •   BUIR Home
      • University Library
      • Bilkent Theses
      • Theses - Department of Computer Engineering
      • Dept. of Computer Engineering - Master's degree
      • View Item
      JavaScript is disabled for your browser. Some features of this site may not work without it.

      Improvements on pathwaymapper: a collaborative pathway curation tool

      Thumbnail
      View / Download
      2.0 Mb
      Author(s)
      Dervishi, Leonard
      Advisor
      Doğrusöz, Uğur
      Date
      2018-07
      Publisher
      Bilkent University
      Language
      English
      Type
      Thesis
      Item Usage Stats
      148
      views
      174
      downloads
      Abstract
      Information 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.
      Keywords
      Graph Visualization
      Pathway Editor
      Systems Biology
      Biological Pathways
      Cancer Genomics
      Pathway Curation Tool
      Web-Based Ssoftware
      Permalink
      http://hdl.handle.net/11693/47683
      Collections
      • Dept. of Computer Engineering - Master's degree 517
      Show full item record

      Browse

      All of BUIRCommunities & CollectionsTitlesAuthorsAdvisorsBy Issue DateKeywordsTypeDepartmentsThis CollectionTitlesAuthorsAdvisorsBy Issue DateKeywordsTypeDepartments

      My Account

      LoginRegister

      Statistics

      View Usage StatisticsView Google Analytics Statistics

      Bilkent University

      If you have trouble accessing this page and need to request an alternate format, contact the site administrator. Phone: (312) 290 1771
      © Bilkent University - Library IT

      Contact Us | Send Feedback | Off-Campus Access | Admin | Privacy