MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.

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I don't know about Skeinforge, but in Slic3r, I can set a different temperatures for the extruder and the bed for the first layer.

I use Repetier-Host as frontend and Slic3r for the slicing. Works very well for me.