Is There Any Free Software To Create Nice Visual Of Ppi Networks Along With Cellular Components?
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10.5 years ago
Diwan ▴ 650

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

ipa ppi • 4.8k views
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Hi, what is IPA?

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10.5 years ago
Woa ★ 2.9k

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

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10.5 years ago

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

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10.5 years ago
Mary 11k

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.

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10.5 years ago
Christian ★ 3.0k

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

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