Saving changes of Cytoscape data in Java(.Jnlp) format

[jinhy...@gmail.com]

Hello, 

I've got analysis results presented in Cytoscape from a company, and now I'm trying to modify and polish the results by myself. 

The results were provided as .jnlp format. 

The size of the file is only 4kb, and I can simply execute it and it automatically initiates "Cytoscape v2.8.3 webstart"

There is a small tab under "results panel" window and I can load expected datasets by clicking on it. 

The problem I faced is basically I cannot save all the changes I made. 

When I tried to save the results using "file>Save as" tab, it generates a 82kb file with .cys extension. 

But when I open it with either Cytoscape v.2.8.3 or Cytoscape v3.4.0 from my MAC, it does not have any data in it. 

I also tried various "export" option.

But it only generates some text files or screenshot. 

Is there any way that I can store my changes if I start from .jnlp file format?

I would like to save the whole analysis results, not just screenshots. 

Any advices will be very helpful. 

Thank you very much!!!

Best, 

Hyun Yong

[Tim Hull]

What data are you expecting to save that isn't? Saving as a .cys should save the networks in the current session - is that not happening? The contents of the Results panel doesn't save - to get that back you will have to re-run whatever plugin the JNLP is using.

Tim

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[jinhy...@gmail.com]

Dear Tim, 

Thanks for reply.

Saving as .cys file generate .cys file as expected. 

However, when I opened it either using Cytoscape 2.8.3 or Cytoscape 3.4.0, 2.8.3 showed following error message and 3.4.0 opened with empty window as follow.

Is this because the data used for the cityscape analysis is stored in the company's server, not in my hard drive?

Best, 

Hyun Yong

On Wednesday, July 20, 2016 at 8:53:16 AM UTC-7, Tim Hull wrote:

What data are you expecting to save that isn't? Saving as a .cys should save the networks in the current session - is that not happening? The contents of the Results panel doesn't save - to get that back you will have to re-run whatever plugin the JNLP is using.

Tim

On Tue, Jul 19, 2016 at 5:12 PM, <jinhy...@gmail.com> wrote:

Hello, 

I've got analysis results presented in Cytoscape from a company, and now I'm trying to modify and polish the results by myself. 

The results were provided as .jnlp format. 

The size of the file is only 4kb, and I can simply execute it and it automatically initiates "Cytoscape v2.8.3 webstart"

There is a small tab under "results panel" window and I can load expected datasets by clicking on it. 

The problem I faced is basically I cannot save all the changes I made. 

When I tried to save the results using "file>Save as" tab, it generates a 82kb file with .cys extension. 

But when I open it with either Cytoscape v.2.8.3 or Cytoscape v3.4.0 from my MAC, it does not have any data in it. 

I also tried various "export" option.

But it only generates some text files or screenshot. 

Is there any way that I can store my changes if I start from .jnlp file format?

I would like to save the whole analysis results, not just screenshots. 

Any advices will be very helpful. 

Thank you very much!!!

Best, 

Hyun Yong

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[Tim Hull]

It sounds like there may be a glitch happening when the session is saved, causing the networks to be unusable. One thing you could try is renaming the network to something shorter, as it looks like the session parser may be choking on the session name. If that doesn't work, try exporting each individual network as an XGMML file and then importing those into 2.8.3 or 3.4 (I'd use 3.4 unless you have a need for a plugin only in 2.8.3).  

Does this get you what you need?

Tim

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[jinhy...@gmail.com]

Thank you very much Tim, 

I will definitly try troubleshooting following your suggestion and see what happens!!

Best, 

Hyun Yong

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