3DScape is a three-dimensional (3D) visualization plug-in for Cytoscape (Shannon et al., 2003). It is a freely available open source Java application licensed under the terms of [LGPL](http://www.gnu.org/licenses/lgpl.html). The extra dimension in 3DScape offers more flexibility for hierarchical or layered representation in Cytoscape. Because its visualization and layout functions are implemented in C++, it is very fast, even networks with several thousand of nodes can be rendered in real time.
1. Convert Cytoscape network view to a 3D. This process can retain the color, size, and shape of nodes.
2. Three-dimensional layout using Fruchterman-Reingold (Fruchterman et al., 1991), Fast Multipole Multilevel Method (FM3) (Hachul et al., 2004), and Span Tree algorithms.
3. Network edges can be rendered in gradient heat map colors, with glowing effect.
4. Animation loops from time points of a series of expression data.
###How to use
3DScape is consisted of one jar file as a Cytoscape plugin and libraries for VTK renderer. Please follow instructions for manual installation on [Microsoft Windows](http://scape3d.sourceforge.net/scape3d_install.html), [Linux](http://scape3d.sourceforge.net/scape3d_install_linux.html), and [Mac OSX](http://scape3d.sourceforge.net/scape3d_install_macos.html). You will also need this [user manual](http://scape3d.sourceforge.net/scape3d_manual.html) on how to use it.
We plan to implement a 3D layout of and interaction with biological networks using subcellular localization annotation, like Cerebral (Barsky et al., 2007). If you are interested or have good suggestions, please feel free to contact us by our email qwang.big[at]gmail.com.
* Shannon, P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504.
* Fruchterman, T.M.J. et al. (1991) Graph Drawing by Force-Directed Placement. Software: Practice and Experience. 21(11).
* Hachul, S. et al. (2004) Drawing large graphs with a potential-ﬁeld-based multilevel algorithm. In Proc. 12th Int. Symp. on Graph Drawing, volume 3383 of LNCS, Springer-Verlag, pp 285–295.
* Barsky, A. et al. (2007) Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics. 23(8):1040-2.
Wang, Qi. 3DScape: three dimensional visualization plug-in for Cytoscape. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2011.6094.1> (2011)