How could I run Cytoscape in non-graphical mode?

[THL]

I run Cytoscape with a script on command line, and Cytoscape is shown with GUI.
Adding -noView option does not make any difference.

So how could I run Cytoscape in non-graphical mode (not showing Cytoscape at all)?

Thanks a lot for your help!

[Barry Demchak]

Hi --

I'm afraid there is no non-graphical mode. The Cytoscape automation choices all involve having Cytoscape visible and updating its visual display. Within that, there are choices ... it sounds like you have found the command line feature. There is also cyREST, which allows program control of Cytoscape .. https://f1000research.com/articles/4-478/v1

Does this help?

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[THL]

Thank you very much for your response!

So if using cyREST, does Cytoscape still display?

BTW, I saw the "-noView" option from Cytoscape 2.1 manual and I am not sure what it means.


The reason I want to have Cytoscape not displayed is that I will eventually display the network that was exported from Cytoscape on Cytoscape.js.

Do you also know Cytoscape.js very well? Initially I just wanted to use Cytoscape.js since we want to put our workflow on the website. But I tried different layout options of Cytoscape.js (random, grid, circle, cose, breadthfirst) and none of these layout options is able to place our molecular network in a layout as nicely as Cytoscape does. I feel that Cytopscape has a very good default nodes placement algorithm which is very suitable for molecular networks.

So now I have to use Cytoscape to do the nodes placement first and then export the JSON file with nodes positions for Cytoscape.js to display on the website.

So do you know if Cytoscape.js also has a default layout algorithm which creates the same nice layout as Cytoscape?

Thanks a lot!

On Sunday, March 5, 2017 at 9:01:48 AM UTC-8, Barry Demchak wrote:

Hi --

I'm afraid there is no non-graphical mode. The Cytoscape automation choices all involve having Cytoscape visible and updating its visual display. Within that, there are choices ... it sounds like you have found the command line feature. There is also cyREST, which allows program control of Cytoscape .. https://f1000research.com/articles/4-478/v1

Does this help?

On Sun, Mar 5, 2017 at 8:54 AM, THL <lt...@mit.edu> wrote:

I run Cytoscape with a script on command line, and Cytoscape is shown with GUI.
Adding -noView option does not make any difference.

So how could I run Cytoscape in non-graphical mode (not showing Cytoscape at all)?

Thanks a lot for your help!

--

[Lars Juhl Jensen]

Without having tested it, I imagine it should be possible to start a Cytoscape under Linux, which uses Xdummy, Xvfb, or Xvnc as its display. This would in effect give you a headless Cytoscape that you can then interface with via e.g. cyREST.

On Sunday, March 5, 2017 at 6:01:48 PM UTC+1, Barry Demchak wrote:

Hi --

I'm afraid there is no non-graphical mode. The Cytoscape automation choices all involve having Cytoscape visible and updating its visual display. Within that, there are choices ... it sounds like you have found the command line feature. There is also cyREST, which allows program control of Cytoscape .. https://f1000research.com/articles/4-478/v1

Does this help?

On Sun, Mar 5, 2017 at 8:54 AM, THL <lt...@mit.edu> wrote:

I run Cytoscape with a script on command line, and Cytoscape is shown with GUI.
Adding -noView option does not make any difference.

So how could I run Cytoscape in non-graphical mode (not showing Cytoscape at all)?

Thanks a lot for your help!

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[Barry Demchak]

Hi –

 

Cytoscape will display regardless of how it’s called.

 

Generally, this hasn’t held developers back.

 

In fact, Cytoscape and Cytoscape.js do not share layout algorithms … they’re really two independent products sharing a common purpose and long term development.

 

As to what constitutes nice layout, that’s a matter of judgment and purpose. I think a number of people have enjoyed CoSE, but it’s still a matter of purpose and taste.

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