Metscape: cannot build network

[Nadia]

Hello,

I'm a new cytoscape user (v3.4.0 with java version: 1.8.0_101) and I'm using the metscape app to import a correlation matrix to build a network but I'm having troubles with importing a matrix format as formatted in the attachment (test.xls). I open metscape and select the file "test.xls" at the input tab (see picture metscape) but I'm never able to push the build network button.

Hope you can help.

Thank you, 

Nadia

[Tim Hull]

I'm having no problems building a network with that file - when I import it, the Build Network is enabled, and the "Range of Edges" values look different. Are you sure this example will reproduce the problem? If this won't reproduce the problem, we need one that will in order to know what's going on.

If you do have the problem with this file, I'd try updating MetScape and Cytoscape to the current version if you haven't already. 

Also, the MetScape team may be able to help you further on this matter - I've CCed them on this email.

Hope this helps...

Tim

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[Nadia]

Yes this example reproduces the problem. I can load the file but I cannot push the "Build network" button as seen on the picture I uploaded in the first message, there I used the test file.

When I send my problem here, I had freshly installed cytoscape, metscape and java so everything should be up-to-date.

Kind regards,

Nadia

Op vrijdag 5 augustus 2016 21:46:10 UTC+2 schreef Tim Hull:

I'm having no problems building a network with that file - when I import it, the Build Network is enabled, and the "Range of Edges" values look different. Are you sure this example will reproduce the problem? If this won't reproduce the problem, we need one that will in order to know what's going on.

If you do have the problem with this file, I'd try updating MetScape and Cytoscape to the current version if you haven't already. 

Also, the MetScape team may be able to help you further on this matter - I've CCed them on this email.

Hope this helps...

Tim

On Wed, Aug 3, 2016 at 12:51 PM, Nadia <njt.r...@gmail.com> wrote:

Hello,

I'm a new cytoscape user (v3.4.0 with java version: 1.8.0_101) and I'm using the metscape app to import a correlation matrix to build a network but I'm having troubles with importing a matrix format as formatted in the attachment (test.xls). I open metscape and select the file "test.xls" at the input tab (see picture metscape) but I'm never able to push the build network button.

Hope you can help.

Thank you, 

Nadia

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[Tim Hull]

Are you doing anything besides opening the correlation-based network build screen and pressing the Browse button to locate test.xls? I do that, and it works fine (on both Mac and Windows). Just want to figure out if there are any other steps that may be causing the problem.

I any case, I'd get in touch with the MetScape team (metsca...@umich.edu), as they would know more about what is going on. I used to work on MetScape, but it's been 4 years and there are a lot of new features at this point (such as correlation-based network). In any case, it may help to run Cytoscape from the command line and see if there are any exceptions being thrown.

Tim

On Tue, Aug 9, 2016 at 4:42 AM, Nadia <njt.r...@gmail.com> wrote:

Yes this example reproduces the problem. I can load the file but I cannot push the "Build network" button as seen on the picture I uploaded in the first message, there I used the test file.

When I send my problem here, I had freshly installed cytoscape, metscape and java so everything should be up-to-date.

Kind regards,

Nadia

Op vrijdag 5 augustus 2016 21:46:10 UTC+2 schreef Tim Hull:

I'm having no problems building a network with that file - when I import it, the Build Network is enabled, and the "Range of Edges" values look different. Are you sure this example will reproduce the problem? If this won't reproduce the problem, we need one that will in order to know what's going on.

If you do have the problem with this file, I'd try updating MetScape and Cytoscape to the current version if you haven't already. 

Also, the MetScape team may be able to help you further on this matter - I've CCed them on this email.

Hope this helps...

Tim

On Wed, Aug 3, 2016 at 12:51 PM, Nadia <njt.r...@gmail.com> wrote:

Hello,

I'm a new cytoscape user (v3.4.0 with java version: 1.8.0_101) and I'm using the metscape app to import a correlation matrix to build a network but I'm having troubles with importing a matrix format as formatted in the attachment (test.xls). I open metscape and select the file "test.xls" at the input tab (see picture metscape) but I'm never able to push the build network button.

Hope you can help.

Thank you, 

Nadia

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[Nadia]

I open cytoscape, go to Apps--> Metscape --> Build Network --> Correlation based. The correlation-based network build screen opens and I press the Browse button to locate test.xls file but than I cannot push the build network button.

I contacted the Metscape team for help so I hope they know how to solve this. 

Op dinsdag 9 augustus 2016 20:03:47 UTC+2 schreef Tim Hull:

Are you doing anything besides opening the correlation-based network build screen and pressing the Browse button to locate test.xls? I do that, and it works fine (on both Mac and Windows). Just want to figure out if there are any other steps that may be causing the problem.

I any case, I'd get in touch with the MetScape team (metsca...@umich.edu), as they would know more about what is going on. I used to work on MetScape, but it's been 4 years and there are a lot of new features at this point (such as correlation-based network). In any case, it may help to run Cytoscape from the command line and see if there are any exceptions being thrown.

Tim

On Tue, Aug 9, 2016 at 4:42 AM, Nadia <njt.r...@gmail.com> wrote:

Yes this example reproduces the problem. I can load the file but I cannot push the "Build network" button as seen on the picture I uploaded in the first message, there I used the test file.

When I send my problem here, I had freshly installed cytoscape, metscape and java so everything should be up-to-date.

Kind regards,

Nadia

Op vrijdag 5 augustus 2016 21:46:10 UTC+2 schreef Tim Hull:

I'm having no problems building a network with that file - when I import it, the Build Network is enabled, and the "Range of Edges" values look different. Are you sure this example will reproduce the problem? If this won't reproduce the problem, we need one that will in order to know what's going on.

If you do have the problem with this file, I'd try updating MetScape and Cytoscape to the current version if you haven't already. 

Also, the MetScape team may be able to help you further on this matter - I've CCed them on this email.

Hope this helps...

Tim

On Wed, Aug 3, 2016 at 12:51 PM, Nadia <njt.r...@gmail.com> wrote:

Hello,

I'm a new cytoscape user (v3.4.0 with java version: 1.8.0_101) and I'm using the metscape app to import a correlation matrix to build a network but I'm having troubles with importing a matrix format as formatted in the attachment (test.xls). I open metscape and select the file "test.xls" at the input tab (see picture metscape) but I'm never able to push the build network button.

Hope you can help.

Thank you, 

Nadia

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[Tim Hull]

Yeah - I'm not having a problem. I'm wondering if MetScape may communicate with a server when the file is loaded - in that case, it could be an issue with your network connection.

Tim

On Wed, Aug 10, 2016 at 1:08 AM, Nadia <njt.r...@gmail.com> wrote:

I open cytoscape, go to Apps--> Metscape --> Build Network --> Correlation based. The correlation-based network build screen opens and I press the Browse button to locate test.xls file but than I cannot push the build network button.

I contacted the Metscape team for help so I hope they know how to solve this. 

Op woensdag 3 augustus 2016 21:51:36 UTC+2 schreef Nadia:

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[Juliana T]

Hey, Nadia. I'm having the  EXACTLY same issues as you. I have installed all the things recently and and i can't build the correlation network. Did you get in touch with Metscape team already? They already answered you? 

Please, let me know if they gave you a solution for this. It's making me crazy. I do everything right and i can't build the network.

Juliana.

[jmde...@googlemail.com]

Hi there

Same problem here. Running cytoscape 3.4.0, JAVA 8_121 under windows 10. And the same problem on another computer with windows 7....