Cytoscape Web Plugin

Cytoscape visualization tool can be used in web applications. Refer to the demo at here: http://cytoscapeweb.cytoscape.org/demos/showcase It can provide good visualizations. Sample snapshot;

Today's Graph: Social Network Visualization

Today's Graph: Social Network Visualization

Graph of Today: US Electricity Network

U.S. electricity network routes

Graph of Today: Twitter Replies

Graph of #slaname tweet messages between October 14, 2009 to December 11, 2009. It is colored and visualized with Processing(http://www.processing.org/).

Graph of 19 October 2012

Reference: Weidong Huang, Colin Murray, Xiaobin Shen, Le Song, Ying Xin Wu, Lanbo Zheng, "Visualisation and Analysis of Network Motifs", in Proccedings 9th International Conference on Information Visualisation (IV05), 2005

The Largest Common Connected Subgraph of the Best Yeast–Human Alignment

The largest common connected subgraph of the best yeast–human alignment. Contains1799 nodes and 3570 edges (approximately 75% of nodes and 22% of edges from the yeast PPI network). An edge between two nodes means that an interaction exists in both species between the corresponding protein pairs.[Memisevic et al, "C-GRAAL: Common-neighbors-based global GRAph ALignment of biological networks"]

PPI Alignment Graph

Scientists recently involved in Network Alignment Topic at Bioinformatic's Networks. People are trying to both find alignments in one path. At another path, people are involved in better visualization outputs. Today, I found a graph for alignment at Milenkovic et al's, "Optimal Network Alignment with Graphlet Degree Vectors". Here, they found shared PPI interactions and nodes of two species. They provide as simple force directed layout output. See the following image:

Yet Another PPI Network

Visualization of the PPIs within two steps away from the epidermal growth factor receptor (EGFR) in humans extracted from the Human Protein Reference Database. The nodes are proteins and the edges represent interactions between them. There are 2331 proteins and 5255 interactions(Taken from http://www.sciencedirect.com/science/article/pii/S1574013709000021)

Protovis: Javascript for nice graph visualizations

Recently, with the increasing interest on web based applications Javascript has born again. With HTML 5 standards, web developers can do even 3D games using browsers capabilities. Protovis is a kind of javascript library to produce nice visualizations. You can visualize your data with many options. You can also adopt arc drawing, force directed drawings, radial drawings to your input graphs. Here are some snapshots from this library: