Is There Any Free Software To Create Nice Visual Of Ppi Networks Along With Cellular Components?

Question

[Diwan]

Hi,

I am able to create decent PPI network pictures with cytoscape. But I recently noticed that IPA can produce nice visual of networks with membranes, cytoplasm, nucleus i.e. it shows different cellular location of proteins as well as interaction between them. But is there any free software that can produce nice visual of PPI along with such cellular components?

I would also like to know which free software do you use to create stunning visuals of networks.

Any comments will be greatly helpful.

Thanks Diwan

[Biojl]

Hi, what is IPA?

[Giovanni M Dall'Olio]

It must be this one: http://www.ingenuity.com/products/ipa/ipa-fall-release-2013

Answer 1

[Woa]

and another one , The Bubble Router http://www.genmapp.org/BubbleRouter/manual.htm

A cytoscape plugin for grouping nodes by 'compartment' ?

Check also Mosaic, and try to partition the network by GO Component http://apps.cytoscape.org/apps/mosaic

Answer 2

[Charles Warden]

I agree IPA is the choice that first comes to mind. I imagine there is probably also some way to do this in cytoscape. Here is a plug-in (which, I admittedly haven't tried) that I found with quick Google search:

http://bioinformatics.oxfordjournals.org/content/23/8/1040.full

Answer 3

[Mary]

Just yesterday there was a bunch of chatter from the Biocuration meeting about Navicell. https://navicell.curie.fr/index.html I haven't tried it out yet, but I'm reading up now. They note that their foundation is the stuff you can do at CellDesigner: http://celldesigner.org/

I had forgotten about CellDesigner--that might be a way to compartmentalize your features.

Answer 4

[Christian]

Since you already work with Cytoscape, you could give the Cytoscape plugin Cerebral a try, which should be able to do this.