Question: Is There Any Free Software To Create Nice Visual Of Ppi Networks Along With Cellular Components?
1
gravatar for Diwan
5.4 years ago by
Diwan560
United States
Diwan560 wrote:

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 • 3.0k views
ADD COMMENTlink modified 9 months ago by zx87547.9k • written 5.4 years ago by Diwan560

Hi, what is IPA?

ADD REPLYlink written 5.4 years ago by Biojl1.7k
1

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

ADD REPLYlink written 5.4 years ago by Giovanni M Dall'Olio26k
2
gravatar for Woa
5.4 years ago by
Woa2.7k
United States
Woa2.7k wrote:

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

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Woa2.7k
1
gravatar for Charles Warden
5.4 years ago by
Charles Warden7.2k
Duarte, CA
Charles Warden7.2k wrote:

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

ADD COMMENTlink written 5.4 years ago by Charles Warden7.2k
1
gravatar for Mary
5.4 years ago by
Mary11k
Boston MA area
Mary11k wrote:

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.

ADD COMMENTlink written 5.4 years ago by Mary11k
1
gravatar for Christian
5.3 years ago by
Christian2.8k
Cambridge, US
Christian2.8k wrote:

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

ADD COMMENTlink written 5.3 years ago by Christian2.8k
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