Question: Network visualisation of json or gml networkx
gravatar for jasperkoehorst
2.4 years ago by
jasperkoehorst10 wrote:

I have created a module which creates a GML file to show the network of the dataset. Now I noticed the visualisation button but unfortunately GML is not (properly) supported. Using the more info button I arrived at this page:

I tried the provided json file but that didn't work either. Is it still supported and if so, in what format?

graph gml visualization json • 632 views
ADD COMMENTlink modified 2.4 years ago by carlfeberhard390 • written 2.4 years ago by jasperkoehorst10
gravatar for carlfeberhard
2.4 years ago by
United States
carlfeberhard390 wrote:

Hi, jasperkoehorst

No - GML is not supported as a) GML isn't a datatype included with Galaxy, and b) GraphVis (and more specifically cytoscapejs) would need to know how to parse it. I haven't been able to find anything on cytoscapejs supporting GML yet - let me know if you find it as that would make things easier.

The JSON example isn't valid JSON unfortunately. You can try this:

  "nodes": [
      "id": 1
      "id": 2
  "links": [
      "source": 1,
      "target": 2

It should work on a plain installation - it's not very exciting though.

The plan going forward is to re-incorporate at least XGMML and SIF datatypes (which are shipped with Galaxy). If you'd want to add the GML datatype and a parser/dataprovider for it - please, let us know - that would be great.

ADD COMMENTlink written 2.4 years ago by carlfeberhard390
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