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Date: Fri, 26 Oct 2012 12:14:39 -0700
Message-ID: <CAOWxDUdy_MiK11t-c5vJp6xuZJL81C6R7QfMb9kmk6L8Xn+...@mail.gmail.com>
Subject: Re: [Cytoscape-discuss] Re: How to export graph from cytoscape to JSON?
From: Keiichiro Ono <kei...@gmail.com>
To: cytoscape-discuss@googlegroups.com
Content-Type: text/plain; charset=ISO-8859-1

Hi everyone.

One of my students is working on project related to this topic.

https://github.com/idekerlab/cyto-bridge/tree/develop

Currently, his code is pushing igraph's "graph" data structure from R
as JSON.  And he've just started to work on the opposite direction:
send CyNetwork and CyTables in JSON (GraphSON) via HTTP.

https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library

This is for Cytoscape 3, but some sort of prototype will be available
by the end of this quarter.

Thanks,
Kei

2012/10/26 Max Franz <maxkfr...@gmail.com>:
> Though I definitely agree it would be great to have more collaborators on
> Cytoscape -- as Alex has mentioned -- here is an alternative that may help
> guide you if you need to do this quickly:
>
> Export the networks in a simple-to-parse format, like SIF.
> In your JavaScript code, parse the exported networks -- creating a resultant
> JavaScript object for each one that can be read in by d3.js, Cytoscape.js,
> or similar.
>
> All the best,
> Max
>
> On Thursday, 25 October 2012 at 13:08, Alexander Pico wrote:
>
> Hi Peter,
>
> It's still on the to-do list. That GSoC project hasn't been picked up yet.
> It's available as a mentored project year-round through our NRNB Academy
> program if you (or anyone else) is interested in taking it on:
>
> http://nrnb.org/academy
>
> One of the main reasons it's on our list is for better communication from
> cytoscape to cytoscape.js, you're right. But as far as I know, it hasn't
> been implemented yet.
>
>  - Alex
>
>
> On Thursday, October 18, 2012 1:45:17 PM UTC-7, Peter wrote:
>
> Dear cytoscape-discuss,
>
> I am trying to help my biologist friend make d3.js visualizations from
> cytoscape network data.
> What's the easiest way to get the network into JSON ?
>
> I'm a bit surprised this information is hard to find: don't the cytoscape.js
> use JSON??
>
> A JSON export plugin was proposed for google Summer of Code 2012, but I
> dunno if it went anywhere:
> https://groups.google.com/d/topic/cytoscape-discuss/J-z3IHHpCto/discussion
>
> Do I do it with a javascript plugin:
> http://wiki.cytoscape.org/ScriptingPlugins#Accessing_Cytoscape_Objects
>
> Help?
>
> Thanks!
>
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-- 
Keiichiro Ono    http://www.keiono.net/