A Cytoscape Plugin For Grouping Nodes By 'Compartment' ?

Question

[Lyco]

Is anybody aware of a possibility (e.g. probably a plugin) to use Cytoscape for representing protein interaction networks in a kind of 'cellular layout' ?

Several pieces of commercial software are offering this option, e.g. by drawing a cell schematic (with nucleus, cytoplasm, plasma membrane, and maybe a few organelles) and then running a layout algorithm where each protein with known localization has to stay within the space reserved for this compartment. Unfortunately, I have not seen any similar for Cytoscape.

For what I currently have in mind, it would be sufficient to define a few boxes on the canvas (by ID and coordinates) and then provide a node attribute that defines where on the canvas the node is allowed to sit. It should then be possible to run a standard layout (e.g. spring-embedded) using the boxes as boundary conditions.

I imagine that I am not the only one who has this idea and that somebody might have tried this before.

[Michael Schubert]

There was an old question about how to draw complexes in Cytoscape, that might help you as well (just do a search).

[Lyco]

This question was also from me. The answer was helpful, but it doesn't really apply here.

[Michael Schubert]

Sorry, didn't recall the details :-)

[cecilia.jimenez-sanchez]

Hello, has anyone achieved to download the Cerebral app?

I have followed their guidelines for installing Cerebral app in Cytoscape:

1: Downloaded both the latest version of cerebral.jar and prefuse.jar from the Cerebral Downloads page. 2: Saved the two files in Cytoscape's apps directory: This PC>local disk©>Program files>Cytoscape V3.6.1>apps

I closed and launched Cytoscape again, but I do not see any Cerebral app in the apps tab.

Can anyone give me a hint on why I cannot see the app?

I know there is a web version but I am not a bioinformatician and I find it very difficult to make the code work.

Thanks a lot!!

[Bartimus]

Check out the "boundaryLayout" app which can be found in the Cytoscape app manager with the default download site (http://apps.cytoscape.org/). This is the closest approximation to Cerebral that I can find. Note that it makes the "cell" round, as opposed to the cross section that Cerebral produces. edit posted as answer

Answer 1

[Stew]

Have a look at Cerebral, which can do layouts based on cellular compartment or any other factor you want to map.

[Lyco]

Thanks for the suggestion, looks exactly like what I need. The only problem is that the download site does not response and every other related page I find by googling either points to that site or something that is just as dead. I will give BubbleRouter a try and if it doesn't solve my problem I will try harder to get a copy of Cerebral.

Answer 2

[Chris Evelo]

You could try the BubbleRouter plugin that is available from the [?] Cytoscape plugin directory[?].

The Bubble Router Plugin allows users to layout a network incrementally and in a semi-automated way. Bubble Router arranges specific nodes in user-drawn regions based on a selected attribute value. Bubble Router works with any node attribute file.

That attribute could be a cellular location. The manual is available [?]here[?].

[Lyco]

Bubble Router looks promising and easy to use. Hoever, it behaves very weird which is probably because the current version is only verified to work with Cytoscape 2.6 while we are running 2.8

[Lyco]

Thank you for this suggestions, looks exactly like what I need. I had looked through the plugin catalog before asking this question, but for some reason I must have overlooked BubbleRouter.

Answer 3

[Mary]

Would any of the Venn tools help with that potentially? There's one I've looked at: http://www.dishevelled.org/venn-cytoscape-plugin/

[Lyco]

I don't think that the VENN tools will help here, but thanks for the suggestion!

Answer 4

[alcotross02]

The application is designed to be easily integrated into any website and is configurable to support customized network visualization. CerebralWeb also supports the automatic retrieval of Cerebral-compatible localizations for human, mouse and bovine genes via a web service and enables the automated parsing of Cytoscape compatible XGMML network files. If you want to know any information about Netgear Arlo security camera just go to https://www.netgearroutersupportnumber.com/netgear-arlo-support/

Answer 5

[Bartimus]

Check out the "boundaryLayout" app which can be found in the Cytoscape app manager with the default download site. This is the closest approximation to Cerebral that I can find. Note that it makes the "cell" round, as opposed to the cross section that Cerebral produces.