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Just as software code is not patentable, because there are so many ways to write code that does the same thing, you should be patenting the application, the method for doing something, not a specific relationship between hardware and software.
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On the shelf today is this application for an "Input device, system and method, " which as mundane as that sounds, actually appears quite the contrary.
ENGADGET
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BranchIt is a cloud application that replaces the desperate email blast with an automated method of discovering who else everyone in the company knows.
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In his presentation, he described how Asterisk, an open-source VoIP application, can be attacked using what he said was an "extremely basic" method known as a buffer overflow.
FORBES: Magazine Article
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For example, the primary method that investment advisors place trades at one major securities brokerage firm is via a Java application.
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