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Per jashkenas, they started with d3/svg, but moved to canvas. I'm guessing this is largely bespoke.

https://news.ycombinator.com/item?id=3988556

It's d3, http://graphics8.nytimes.com/packages/js/newsgraphics/2012/0...

The new app was originally written with d3 but, by the time of deployment d3 was responsible only for scaling the axes, and the rest of the graphic was built largely around custom code written around canvas elements.

Ah, I see in carbocation's link now. It just seems odd to say they moved from d3/svg to canvas, because d3 is just a layer on top of canvas (or the dom), and if you look at their source (not chart.js, the minimized source on the website) it's full of calls to d3 still. Maybe more useful to OP to say that it was originally written in d3, then optimized.

Looks like protovis, unless they are using different tools for each graphic. http://mbostock.github.com/protovis/ex/pack.html