3DScape Intro

  3DScapeCS Intro

  Download 3DScape

  Download 3DScapeCS

  3DScape Manual

  3DScapeCS Manual

  Cytoscape Plugins

  UbiGraph Homepage

3DScapeCS Introduction

Visualization of Three-dimensional Networks

Convert Cytoscape 2D network view to 3D view that retains almost all settings such as colors, sizes, and shapes of all nodes. On double-clicking the node, its attributes will be shown in the Node/Edge Attribute Browser panel. A searching box is provided to users to search the nodes/edges by corresponding identifiers. The nodes that match the searching will be highlighted with a label in the scene.

Three-dimensional Layout

The multilevel layout algorithm implemented in UbiGraph is suitable for large networks, which generates aesthetically pleasing graph layouts with all edges of nearly equal length.

Time-coursed Data Animation

Cytoscape supports the mapping of gene expression data to node color, label, and border thickness. It also creates an animated view of the network for displaying the changes over time in a series of experiments. We also implemented motion network in 3DScapeCS, made it possible to study changes over sub-networks, such as mass spectral molecular networks.

Parallel visualization

The Cytoscape network view can be rendered in UbiGraph on multiple computer clients through network communication. Different client can be set to visualize different aspects of the graph, either a reversal of perspective, or another time-point for time-course animation.

Supplementary Information

3DScapeCS User Manual.
Download 3DScapeCS here.
Install 3DScapeCS.
Tutorial video on youtube: http://www.youtube.com/playlist?list=PLHvmAmvm_7ogwJWM5twK61t4aEzBXpBMc