Re: [Cytoscape-discuss] Path between two nodes

[Tim Kacprowski]

hi,

you can have a look at http://apps.cytoscape.org/apps/shortestpath, for instance

best

tim

____________________________________________

Tim Kacprowski

Molecular Networks in Medical Bioinformatics

Max Planck Institute for Informatics

http://www.medbioinf.de

Campus E1.4, 66123 Saarbrücken, Germany

Phone: +49-681-9325-3022

____________________________________________

On Tue, May 14, 2013 at 6:35 AM, Kumud Agarwal <kumu...@gmail.com> wrote:

Hi

How can I find the path between any two selected nodes in a network?

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[Alexander Pico]

I think this is what you're looking for: PathExplorer. A simple tool for finding all paths from or to a node, or between nodes.

http://apps.cytoscape.org/apps/pathexplorer

 - Alex

[Ugur Dogrusoz]

Hi,

 

Often times one is interested in finding a shortest path between source and target nodes. For this, there are Cytoscape plugins available as pointed out. If you'd like all paths between specified source and target nodes, including not only the shortest ones but those paths linking source to target with a length of the shortest plus some user specified constant, however, take a look at the following paper. These algorithms were implemented in a number of different projects but not within Cytoscape though.

 

U. Dogrusoz, A. Cetintas, E. Demir, and O. Babur, "Algorithms for Effective Querying of Compound Graph-Based Pathway Databases", BMC Bioinformatics, 10:376, 2009.

 

thanks,

Ugur