Cytoscape Web 2 prerelease

[Max Franz]

We are proud to present to you Cytoscape Web 2.

Cytoscape Web 2 is the next generation of graph visualisation technology on the web.  It combines the power and convenience of jQuery -- a very easy-to-learn JavaScript library -- with HTML5 technologies to provide a good experience for developers and end-users alike.

Philosophy : The jQuery philosophy is fully embraced in Cytoscape Web 2.  Not only do the API functions follow jQuery’s conventions, but the concept of collections is also followed.  You can now deal with collections of graph elements in Cytoscape Web just as you would deal with collections of DOM elements in jQuery.

Technology : Cytoscape Web 2 is a jQuery plugin, so it integrates very well with other jQuery widgets and your own jQuery code.  The included renderer in Cytoscape Web 2 uses SVG technology to provide a consistent cross-browser experience, comparable to the performance of the prior Flash-based version.  We’ve even included iOS support so you can pinch to zoom the graph, drag nodes with your finger, and more right out of the box!

Selectors : Use CSS-like selectors as you would in jQuery to query the graph, filter collections of elements, and so on.

Event handling : Event binding is easy in Cytoscape Web 2.  Not only do we support the same API functions for binding as jQuery that you know and love, but we’ve added even more to make developers’ lives easier.

Extensibility : You can write jQuery plugins that provide widgets or other UI in conjunction with an instance of Cytoscape Web.  In addition, you can write extensions to add core functionality to Cytoscape Web 2, including core functions, collection functions, layouts, renderers, and exporters.  We’ll be leveraging the new jQuery plugins site to automatically manage the plugins and extensions that developers write on GitHub.

You can download prerelease snapshots builds of Cytoscape Web 2 with the caveat that we ask you to provide feedback regarding any bugs and usability issues that you come across.  Cytoscape Web 2 is already very reliable, and we hope that with your help we can make it even better!

Thank you to all the supporters of Cytoscape Web; we all have a lot to look forward to in the near future.

All news and discussion for Cytoscape Web 2 can be found on the new Google group, cytoscapeweb.  The old Google groups, cytoscapeweb-announce and cytoscapeweb-discuss, will be maintained for the Flash version of Cytoscape Web.

[Nikhil Reddy Podduturi]

Thank you Max for the effort.

Once I go through the documentation, I will try it out and let you know.

-Nik

[Max Franz]

We're also looking for people interested in participating in Google Summer of Code.  Cytoscape Web 2 is participating under NRNB in GSOC, and we have some suggested ideas already.

For those unfamiliar with GSOC, it's an opportunity for students to participate in open-source projects while being financially compensated by Google.

Feel free to suggest new ideas in your proposals.  The more students that participate in GSOC for Cytoscape Web, the better.

If you have any questions, please feel free to use the group.

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[Giles Weaver]

Hi Max,

This looks like a massive improvement on the original Cytoscape Web, well done! I have to admit to really disliking the original versions use of Flash, and had been looking into drawing networks using Processing.js (it is very fast for drawing nodes). I will now reconsider!
That said, if performance becomes an issue it may be worth looking at using Processing.js in Cytoscape Web. I had Processing.js draw and animate a thousand nodes and it was very smooth (in Chromium only, unfortunately).
I'll have a play when some layout plugins are available.

Giles

[Max Franz]

There are already two force-directed layout extensions using arbor.js and springy.js.

Processing.js looks interesting, though.  It would be possible to write a renderer using it.  It looks like it uses canvas without WebGL, though, and there are significant performance increases -- about an order of magnitude -- by using WebGL. 

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[Giles Weaver]

Excellent, the plugins existence wasn't obvious to me from the website. I have yet to download the code and have a look around.

Apparently Processing.js does have support for WebGL - see http://processingjs.org/articles/RenderingModes.html
I can't see the WebGL content on that page though - I don't think my browsers support WebGL (on Linux, without tweaking).

G

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[Giles Weaver]

I spoke too soon - a quick trip to about:config in Firefox and I have Processing.js rendering using WebGL (on Ubuntu 11.10 with Intel Core i3-2120 graphics).
G

[Max Franz]

Sounds good.  It's probably a good option for another renderer, because it will abstract the drawing technology (canvas 2D, WebGL).  This will help to future-proof the renderer:  We'll be able to pull in updates from Processing.js such that when new rendering technology comes out, we won't have to change the renderer code.

If you're interested in helping us work on a renderer using Processing.js, please let us know.  We can give you direct commit privileges to Cytoscape Web 2 on GitHub.

[Rudy Bonefas]

I'm pretty excited about this from the description alone. I've been using the Flash version and have been a little frustrated with it.  I know from using a  commercial graph package, mxGraph, on a previous project how much richer the rendering possibilities are with SVG combined with HTML.  Gonna take a look at the code now, hopefully you put some though into making the transition from the Flash version to the this version a smooth experience.    

On Wednesday, March 28, 2012 1:37:02 PM UTC-4, Max Franz wrote: