Problem installing FM3 Layout plugin

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Victoria Challinor

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Jan 10, 2017, 7:51:25 AM1/10/17
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Hello,

I am having trouble installing this FM3 layout plugin:


I copied the .jar file to the apps folder, but FM3 doesn't seem to be available when I reopen Cytoscape. I also looked for FM3 through the App Manager in Cytoscape but couldn't find it there.

I'm using Cytoscape 3.5.0-RC1 on MacOS Sierra 10.12.1.

Thanks for any tips!

Regards,
Victoria

piet molenaar

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Jan 10, 2017, 8:05:08 AM1/10/17
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Hi Victoria,
This is a plugin that is unfortunately only compliant with version 2.6 of Cytoscape.
Is there a special reason you want to use this layout?
Cheers,
Piet


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Piet Molenaar
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Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

Victoria Challinor

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Jan 10, 2017, 8:12:06 AM1/10/17
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Hi Piet,

Thanks for your quick response. I wanted to use FM3 because it is often cited in molecular networking papers and tutorials, for example this one:


Is there any particular layout that you would recommend using as an alternative?

Cheers,
Victoria


On Tuesday, 10 January 2017 14:05:08 UTC+1, Piet wrote:
Hi Victoria,
This is a plugin that is unfortunately only compliant with version 2.6 of Cytoscape.
Is there a special reason you want to use this layout?
Cheers,
Piet

On Tue, Jan 10, 2017 at 1:51 PM, Victoria Challinor <v.cha...@gmail.com> wrote:
Hello,

I am having trouble installing this FM3 layout plugin:


I copied the .jar file to the apps folder, but FM3 doesn't seem to be available when I reopen Cytoscape. I also looked for FM3 through the App Manager in Cytoscape but couldn't find it there.

I'm using Cytoscape 3.5.0-RC1 on MacOS Sierra 10.12.1.

Thanks for any tips!

Regards,
Victoria

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piet molenaar

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Jan 10, 2017, 9:06:59 AM1/10/17
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Hi Victoria,
It depends a bit on what you want to achieve, but most of the time I start by using the default layout within cytoscape, prefuse force directed. The yFiles>organic can give nice results also.
Next I usually include attribute values of either nodes or edges as input for the force directed variants of the layouts. 
Hope this helps,
Piet

On Tue, Jan 10, 2017 at 2:12 PM, Victoria Challinor <v.cha...@gmail.com> wrote:
Hi Piet,

Thanks for your quick response. I wanted to use FM3 because it is often cited in molecular networking papers and tutorials, for example this one:


Is there any particular layout that you would recommend using as an alternative?

Cheers,
Victoria


On Tuesday, 10 January 2017 14:05:08 UTC+1, Piet wrote:
Hi Victoria,
This is a plugin that is unfortunately only compliant with version 2.6 of Cytoscape.
Is there a special reason you want to use this layout?
Cheers,
Piet

On Tue, Jan 10, 2017 at 1:51 PM, Victoria Challinor <v.cha...@gmail.com> wrote:
Hello,

I am having trouble installing this FM3 layout plugin:


I copied the .jar file to the apps folder, but FM3 doesn't seem to be available when I reopen Cytoscape. I also looked for FM3 through the App Manager in Cytoscape but couldn't find it there.

I'm using Cytoscape 3.5.0-RC1 on MacOS Sierra 10.12.1.

Thanks for any tips!

Regards,
Victoria

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For more options, visit https://groups.google.com/d/optout.



--
Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

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Victoria Challinor

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Jan 10, 2017, 9:26:40 AM1/10/17
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Thanks, that was really helpful! I'll play around with the different layouts you mentioned.

Cheers,
Victoria
Hi Piet,
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.
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For more options, visit https://groups.google.com/d/optout.



--
Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

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