 |
 |
 |
 |
 |
The First GPU-accelerated Cytoscape Plugin.
Please enjoy our free GPU Computing Service with AllegroMCODE.
AllegroMCODE is a high-performance Cytoscape plugin to find clusters, or highly interconnected groups of nodes in a huge complex network such as a protein interaction network and a social network in real time. AllegroMCODE finds the same clusters as the MCODE plugin does, but the analysis usually takes less than a second even for a large complex network. The plugin user interface of AllegroMCODE is based on MOCDE and has additional features. AllegroMCODE is an open source software and freely available under LGPL.
Cluster has various meanings according to the sources of networks. For instance, a protein-protein interaction network is represented as proteins are nodes and interactions between proteins are edges. Clusters in the network can be considered as protein complexes and functional modules, which can be identified as highly interconnected subgraphs. For social networks, people and their relationships are represented as nodes and edges, respectively. A cluster in the network can be considered as a community which has strong inter-relationship among their members.
AllegroMCODE exploits our high performance GPU computing architecture to make your analysis task faster than ever. The analysis task of the MCODE algorithm to find the clusters can be long for large complex networks even though the MCODE is a relatively fast method of clustering. AllegroMCODE provides our parallel algorithm implementation base on the original sequential MCODE algorithm. It can achieve two orders of magnitude speedup for the analysis of a large complex network by using the latest graphics card. You can also exploit the GPU acceleration without any special graphics hardware since it provides the seamless remote processing in our free GPU computing server.
You do not need to purchase any special GPU hardware or systems and also not to care about the tedious installation task of them. All you have to do are to install the AllegroMCODE plugin module on your computer and create a free account on our server.
MCODE is the cluster finding algorithm plugin which is developed by the Bader Lab at the University of Toronto. You can get detailed information from http://baderlab.org/Software/MCODE
Cytoscape is a popular network visualization and analysis software and is freely available. You can download Cytoscape and get detailed information from http://www.cytoscape.org.
|
■ Installatioion
|
|
Yon can install the AllegroMCODE plugin through the Cytoscape plugin manager under the "Analysis" category or manually install it by coping AllegroMCODE-1.0.jar into the "plugins" folder in your Cytoscape installation folder. You can also download the source codes: AllegroMCODE-source-1.0.zip.
|
■ Features
|
■ Screen Shot
|
■ Performance: AllegroMCODE vs. MCODE
■ Publication
Jun S. Yoon and Won-Hyung Jung, "A GPU-accelerated bioinformatics application for large-scale protein interaction networks", APBC poster presentation, 2011.
■ Screencasts (Youtube Movie)
[ Installation & Uninstallation ]
[ User Guide ]
[ Processing Speed: AllegrMCODE vs. MCODE ]
|
| |
|
