Gephi/Cytoscape

[Dirk Krueger]

Dear Cytoscape Team,
are there ways to export files that are readable by other network analysis tools and editors, especially the Pajek and GML formats seem to be useful?
In particular, the manual says that GML reading is supported by Cytoscape. For exporting, my Cytoscape 3.0.1 lists only nnf, PSI-MI, sif and xgmml listed. The latter also is not readable by Gephi.
Thank you for advice on this issue.
Dirk

[Keiichiro Ono]

Hi.

Both Gephi and Cytoscape support GraphML, and it's widely used graph
file format these days. I recommend to use GraphML if you need to use
multiple tools in your workflow. This is not limited to visualization
tools. I think most of the common toolkits like igraph, NetworkX, or
Tinkerpop layer, also supports GraphML.

Kei

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[Sascha H]

Hi,

As Dirk already said: "For exporting, my Cytoscape 3.0.1 lists only nnf, PSI-MI, sif and xgmml listed". For me it's the same.

How can I export a previously loaded .graphml file again to .graphml?

Thanking you in advance,

Sascha

Am Mittwoch, 9. Juli 2014 19:57:44 UTC+2 schrieb Kei:

Hi.

Both Gephi and Cytoscape support GraphML, and it's widely used graph
file format these days.  I recommend to use GraphML if you need to use
multiple tools in your workflow.  This is not limited to visualization
tools.  I think most of the common toolkits like igraph, NetworkX, or
Tinkerpop layer, also supports GraphML.

Kei



2014-07-09 9:02 GMT-07:00 Dirk Krueger <nasow...@googlemail.com>:
> Dear Cytoscape Team,
> are there ways to export files that are readable by other network analysis
> tools and editors, especially the Pajek and GML formats seem to be useful?
> In particular, the manual says that GML reading is supported by Cytoscape.
> For exporting, my Cytoscape 3.0.1 lists only nnf, PSI-MI, sif and xgmml
> listed. The latter also is not readable by Gephi.
> Thank you for advice on this issue.
> Dirk
>
> --
> You received this message because you are subscribed to the Google Groups
> "cytoscape-helpdesk" group.
> To unsubscribe from this group and stop receiving emails from it, send an

> email to cytoscape-helpdesk+unsub...@googlegroups.com.

[WinLeiKKhine]

Dear Cytoscape Team,

Does anyone help me to export network files in Cytoscape in a format which Pajek can read?

Thank you in advance.

Win

[Lars Juhl Jensen]

I would say that step 1 is to upgrade to a more recent version of Cytoscape - version 3.0.1 is a very old by now. In version 3.7.2 you have access to several additional formats, including GraphML.