Biostar Beta. Not for public use.
Is There Any Free Software To Create Nice Visual Of Ppi Networks Along With Cellular Components?
1
Entering edit mode
20 months ago
Diwan • 560
United States

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 • 2.9k views
ADD COMMENTlink
0
Entering edit mode

Hi, what is IPA?

ADD REPLYlink
1
Entering edit mode
ADD REPLYlink
2
Entering edit mode
10 months ago
Woa ♦ 2.7k
United States

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
1
Entering edit mode
9 months ago
Duarte, CA

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
1
Entering edit mode
4.6 years ago
Mary 11k
Boston MA area

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
1
Entering edit mode
2.3 years ago
Christian ♦ 2.8k
Cambridge, US

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

ADD COMMENTlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1