PMC

Visualization of expression data. Comparing 2D and 3D expression data visualization using VistaClara and 3DScapeCS using VistaClara heat map scheme. (a,d) gal1RGexp, (b,e) gal4RGexp, (c,f) gal80Rexp.

Visualization of metabolic flux data in a substrate-product network. Metabolic flux simulation in FluxMap (a-c) and 3DScapeCS (d-f), a-f represents different genotypes. (a,d) WT, (b,e) “KO R08”, (c,f) “KO R09”.

The 3DscapeCS interface. Running 3DscapeCS in Cytoscape. (a) 3DScapeCS control panel; (b) Selected nodes/edges are listed in Attribute Browser; (c) Test data converted into 3D view using UbiGraph; (d) Corresponding 2D view in Cytoscape.

Mass spectrometry (MS) motion network with six conditions. a-e are snapshots of the motion network at different dose treatments using avermectin. f was treated with DMSO, which served as a negative control.

Visualization of contig relationships. Comparing 2D and 3D contig relationships visualization generated using ContigScape. Red circles show 27 connections with 5' end of contig No. 510 and 30 connections with 3' end of contig No. 510 in 3DScapeCS (left) and Cytoscape (right), respectively.

Visualization of metabolic flux data in a reaction network. Metabolic flux data for E.coli metabolism are visualized in a reaction network. (a)E.coli metabolism network in Cytoscape. (b)E.coli metabolism network in 3DScapeCS. (c)E.coli metabolism network with simulated data. Each node represents a reaction, with its size corresponding to the reaction rate. The changed reaction found to compare are highlighted with red circles.

Visualization of de Bruijn graphs converted from velvet. Comparing 2D and 3D de Bruijn graph created from LastGraph file generated by Velvet. The bubbles found to compare are highlighted with red ellipse. Bubbles are not clear due to they were overlaid with other nodes or edges (upper) in Cytoscape. They become clear when rotated to a different perspective in 3DScapeCS (lower).