3D Renderer (In Beta)

This is a plugin for Cytoscape 3 that is capable of replacing the default Ding 2D renderer with a 3D renderer. Underneath, it uses the JOGL library which allows access to C/C++ based OpenGL libraries from Java. The renderer is currently under development.

screenshot-0.57.2.png

Current Features

Download

Windows: cytoscape-windows-3.0.0-M4-SNAPSHOT-3d-0.6.zip

Mac, Linux, UNIX OS: cytoscape-unix-3.0.0-M4-SNAPSHOT-3d-0.6.tar.gz

Installation

Windows: Extract the .zip file and run cytoscape.bat.

Mac, Linux, UNIX OS: Extract the .tar.gz file and run cytoscape.sh.

Bird's eye view

Under the Network tab to the left, click or drag the mouse on the bird's eye view display to move the main camera

Visual Properties and VizMapper

For node shapes, the following settings in VizMapper will give the following results:

VizMapper setting

3D result

Ellipse

Sphere

Diamond

Cube

Triangle

Tetrahedron

(New as of v0.52) For edge line types, the following settings give the following results:

VizMapper setting

3D result

Solid

Regular edges

Equal Dash

Dashed edges

Dots

Dotted edges

Camera Controls

Movement:

W

Move up

A

Move left

S

Move down

D

Move right

E

Move forward

Q

Move backward

Rotation:

Z

Roll camera clockwise

X

Roll camera counter-clockwise

Shift + Left

Rotate about Y-Axis, towards the left

Shift + Right

Rotate about Y-Axis, towards the right

Shift + Up

Rotate about X-Axis, upwards

Shift + Down

Rotate about X-Axis, downwards

First-person camera turning:

Left

Turn camera left

Right

Turn camera right

Up

Tilt camera upwards

Down

Tilt camera downwards

Network Manipulation Controls

Node, edge addition and removal:

N

Creates a new node under the mouse cursor

J

Creates a new edge between currently selected nodes and the node currently under the mouse cursor

Delete

Removes currently selected nodes and edges

Selection:

Node dragging:

Miscellaneous Controls

K

Toggle frames-per-second display at bottom left of network window

L

Toggle rendering all node labels or only labels of selected nodes and nodes under the mouse cursor

Currently Supported Visual Properties

Nodes:

Edges:

Network:

Lighting (Under "Network" category)

Planned Features

Source Code

The source code for the 3D renderer plugin may be found at the following SVN repository: http://chianti.ucsd.edu/svn/csplugins/trunk/toronto/yuedong/paperwing-impl

Known Issues

Cytoscape Redmine Page

The Redmine page for the renderer is: http://code.cytoscape.org/redmine/projects/3d-renderer

Contact

I can be found in my post on the Cytoscape mailing list: http://groups.google.com/group/cytoscape-discuss/browse_thread/thread/aae8bb3d265d0ced

Version History

March 30, 2012

v0.6

March 19, 2012

v0.58

March 5, 2012

v0.57.2

February 11, 2012

v0.57.1

February 10, 2012

v0.57

February 6, 2012

v0.55

January 31, 2012

v0.52

January 24, 2012

v0.5: Initial beta release

Cytoscape_3/3D_Renderer (last edited 2012-03-29 21:34:52 by YueDong)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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