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I am a computer science major who has a lot of theoretical classes that involve a lot of math. I hate using pen and paper for scratch work because I keep on losing them so I am planning on getting a new bamboo input tablet so that I can do all the "scratch work" in an accessible format on my laptop. However, I am finding it hard locating an application in Linux that essentially acts as an accessible white board. All of the apps I look at are geared towards artists and so are not designed to accommodate my needs. Is there an app geared to people who have requirements like mine?

P.S I already use latex but that is usually for work already done and thus not very effective for the things that I am still figuring out.

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Try using Xournal:

Xournal is an application for notetaking, sketching, keeping a journal using a stylus. It is free software (GNU GPL) and runs on Linux (recent distributions) and other GTK+/Gnome platforms. It is similar to Microsoft Windows Journal or to other alternatives such as Jarnal, Gournal, and NoteLab.

Xournal screenshot

Or if you don't mind a Java app, Jarnal:

Jarnal is an open-source application for notetaking, sketching, keeping a journal, making a presentation, annotating a document - including pdf - or collaborating using a stylus, mouse or keyboard. It is similar to Microsoft Windows Journal and to the earlier Mimeo whiteboarding and Palm notepad applications.

Jarnal screenshot

However, they are not so much of a whiteboard, but much more like note-taking applications.

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You beat me to it, I thought of Xournal too when I saw the question but couldn't remember its name. I've used it before and it's pretty good for this kind of use. –  Michael Kjörling Apr 28 '12 at 20:10
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