Are There Open Source Js Libraries For The Depiction Of Pathways?

Question

[Nico Adams]

Dear All,

I am looking for an open souce JavaScript Library that would allow the in browser depiction of pathways I really don't want to pre-generate static images and embed those in a web page, if I can avoid it. Is anybody aware of any resource in this area and could point me? Thanks for your help!

[Fred Fleche]

Could you add some details to your question please. Actually I build some interactive KEGG pathways using SVG and Javascript but I don't know if it is what you are looking for.

Answer 1

[Pierre Lindenbaum]

In my bookmarks:

• Protovis
• http://live.yworks.com/yfiles-ajax/Examples/Graph_Viewer.html
• http://thejit.org/static/v20/Jit/Examples/ForceDirected/example1.html
• http://www.kylescholz.com/blog/2006/10/jsviz_031_available.html
• I also liked the FoafNaut but it seems down: http://www.jibbering.com/2004/7/foafnaut-theyrule.JPG

and you could also use something like a remote graphviz dot server to generate your images on the fly:

• http://www.graphviz.org/Misc/webdot.pl

[Nico Adams]

Hehe strane situation - I would like to accept both Pierre's and Brad's answers....all of these suggestions are very valuable. Thanks guys....

[Nico Adams]

Strange situation - I would like to accept both Pierre's and Brad's answers....all of these suggestions are very valuable, but unfortunately there can be only one it seems. Thanks guys....

Answer 2

[Brad Chapman]

Cytoscape Web uses Javascript and Flash. The Pathguide example in the demos might be a useful place to get started:

http://cytoscapeweb.cytoscape.org/demo

JavaScript InfoVis Toolkit has a few different graph and tree representations you could use to show pathways:

http://thejit.org/demos/

If you wanted to code your own with full control, Processing.js provides a nice framework:

http://processingjs.org/

[Nico Adams]

Hi Brad, thanks for that. I had thought of hacking the jit into shape as well - was just wondering whether there were a few more bespoke tools

[Brad Chapman]

No problem, wish I knew a more specific tool to suggest. It'll be interesting to hear if others come up.

Answer 3

[Chris Evelo]

It is not Javascript, but PathVisio has a html exporter (in beta) that allows visualization of data and clickable backpage information (connected database information for genes and metabolites). See http://www.pathvisio.org/wiki/PluginDocumentation.