Bipartite Graphs

[Saatviga Sudhahar]

Hi,

Does anybody know if there is a plug-in for Cytoscape to generate a bipartite graph?
I'm trying to create a bipartite graph with the interacting nodes and edges.

Thanks
Saatviga S.

[nickfyson]

You could try the following Cytoscape plugin, it might do what you're
after...

http://bilayout.bioinf.mpi-inf.mpg.de/index.php

[James Prabhakaran]

[Matthias König]

You could generate your network as SBML which is by design bipartite (species and reactions) and than import the SBML in Cytoscape (CySBML). There are good tools for SBML generation like Antimony or you can write the SBML programatically.

http://sbml.org/Main_Page
http://www.charite.de/sysbio/people/koenig/software/cysbml/
http://antimony.sourceforge.net/main.html

Matthias

[Nader Fathzadeh]

This version doesn't work with cytoscape 3 ...

looking for a plugin for latest version of cytoscape.

[Matthias König]

Hi Nader,

Cytoscape 3 version is available here
https://github.com/matthiaskoenig/cy3sbml
and in the app store
http://apps.cytoscape.org/apps/cy3sbml

To create a simple bipartite SBML graph in python with tellurium use

import tellurium as te

ant = """
model graph()
    // bipartite reaction-species graph (R-S graph)
    // all ingoing edges on the left, outgoing on the right
    R1: A + B => C;
    R2: C => D;
    R3: D => E;
end
"""

sbml = te.antimonyToSBML(ant)
with open("bipartite-graph.xml", "w") as f:
    f.write(sbml)

Than load the SBML with cy3sbml:


Hope this helps.
Matthias