i-Vis @ Bilkent

Information Visualization Research Lab
at Bilkent University

Ugur Dogrusoz

Big data visualization & analytics, Pathway visualization & informatics, Graph drawing & layout, Graph database querying algorithms

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Example Applications

  • Understanding human metabolism and disease conditions through biological pathway analysis
  • Identifying fraud in financial networks
  • Management and monitoring of computer networks
  • Understanding how people behave and collaborate online to improve web sites through social network analysis
  • Detecting and monitoring of terrorist or criminal networks via telecommunication network analysis

Cerami, Gao, Dogrusoz et al., The cBio Cancer Genomics Portal: An open source platform for exploring multi-dimensional cancer genomics data, Cancer Discovery, 2012

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Graph Queries

  • Access database to get a “graph/network of interest” from “nodes of interest”
  • Graph algorithms
    • Shortest paths
    • Neighborhoods
    • Common targets / sources
    • Centrality
    • Often requires variations (e.g. shortest + k length paths)

Dogrusoz et al., Algorithms for Effective Querying of Compound Graph-Based Pathway Databases, BMC Bioinformatics, 2009

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Automatic Graph Layout

Automatic layout of compound / nested graphs

Automatic layout of clustered / grouped graphs

Dogrusoz et al., "A Layout Algorithm For Undirected Compound Graphs", Information Sciences, 179, pp. 980-994, 2009.

Dogrusoz et al., "CiSE: A Circular Spring Embedder Layout Algorithm", IEEE Transactions on Visualization and Computer Graphics, 19(6), pp. 953-66, 2013.

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Complexity Management

Hide-show: hide currently non-interesting parts and reveal on demand

Expand-collapse: collapse groups / clusters to later expand on deman

Dogrusoz et al., "A Multi-Graph Approach to Complexity Management in Interactive Graph Visualization", Computers & Graphics, 30(1), pp. 86-97, 2006.

Dogrusoz et al., "Efficient methods and readily customizable libraries for managing complexity of large networks", PLOS ONE, 13(5): e0197238, 2018.

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Evolving Networks

Time based filtering and animation

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Collaborators

Certain company

Certain company

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Software Highlights

Pathways simplified: View, design, and analyze pathways in SBGN...

newteditor.org

Sari, Bahceci, Dogrusoz et al., "SBGNViz: a tool for visualization and complexity management of SBGN process description maps", PLOS ONE, 10(6), e0128985, 2015.

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Software Highlights

PathwayMapper

Collaborative pathway curation tool for interactive creation, editing, and sharing of cancer pathways

Bahceci, Dogrusoz, La et al., "PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data", Bioinformatics, 33(14), pp. 2238-40, 2017.

Sanchez-Vega et al., "Oncogenic Signaling Pathways in The Cancer Genome Atlas", Cell, 173(2), pp. 321-337.e10, 2018.

pathwaymapper.org & cbioportal.org

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Software Highlights

cbioportal

Visualization, analysis, and download of large-scale cancer genomics data sets

Gao, Aksoy, Dogrusoz et al., "Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal", Science Signaling, 6(269), pl1, 2013.

Sanchez-Vega et al., "Oncogenic Signaling Pathways in The Cancer Genome Atlas", Cell, 173(2), pp. 321-337.e10, 2018.

cbioportal.org

i-Vis @ Bilkent

Software Highlights

Visuall

A proprietary software library used by companies for commercial purposes

A library to jump start software developers in building a visual web based component for analysis of relational information

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Software Highlights: complexity management

https://js.cytoscape.org/#extensions

Generic plugins for Cytoscape.js used by many to build commercial and non-commercial visualization software

27★ cytoscape.js-view-utilities: hide/show, highlight, zoom

52★ cytoscape.js-expand-collapse: manage complexity with expand-collapse

i-Vis @ Bilkent

Software Highlights: automatic layout

https://js.cytoscape.org/#extensions

Generic plugins for Cytoscape.js used by many to build commercial and non-commercial visualization software

3★ cytoscape.js-layout-utilities: placement of new nodes and polyomino packing of components

3★ cytoscape.js-avsdf: circular layout

3★ cytoscape.js-cise: clustered graph layout

11★ cytoscape.js-fcose: fast compound graph layout

67★ cytoscape.js-cose-bilkent: compound graph layout

i-Vis @ Bilkent

Software Highlights: graph editing

https://js.cytoscape.org/#extensions

Generic plugins for Cytoscape.js used by many to build commercial and non-commercial visualization software

8★ cytoscape.js-edge-editing: reconnection and rerouting of edges

25★ cytoscape.js-undo-redo: undo/redo of graph editing operations

11★ cytoscape.js-node-resize: interactive resizing of nodes

24★ cytoscape.js-grid-guide: grid and guidelines for convenient placement of nodes

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Software Highlights: miscellaneous

https://js.cytoscape.org/#extensions

Generic plugins for Cytoscape.js used by many to build commercial and non-commercial visualization software

7★ cytoscape.js-autopan-on-drag: automatic panning on drag out of drawing canvas

19★ cytoscape.js-graphml: bi-directional conversion between graphml and Cytoscape.js

38★ cytoscape.js-context-menus: context-sensitive menus on graph objects

i-Vis @ Bilkent

Contact

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i-Vis @ Bilkent

i-Vis Research & Development - Google Slides