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In the area of chip design tools almost every "methodology" is patented, which is basically, a computer implementation of diverse textbook algorithms so vaguely phrased that if you ever try to replicate anything nearly similar, you will 100% violate someone's patent (like this one, for instance http://www.google.de/patents/US8621403)

Obviously, if I make a tool to perform such analysis (as described in the patent above) and sell this tool, this is an infringement.

But can I make my own tool for my personal use, and use it to create my final product (a chip), which is not realted to the methodology itself? Is this a patent infringement in this case too?

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If a process is patented, the patent is infringed by activities including carrying out the method, selling a product made directly by the process, making an offer to sell such a product.

Personal research or studies generally is a valid defence, that is, activities within the scope of the claims that would normally infringe are excused if the activities are for these purposes. But commercial activity would remove this defence. So as soon as you offer for sale a chip designed with a patented method there may potentially be an issue.

A possible exception I can think of, is if you have bought a specific tool from a vendor and the end user licence agreement specifically gives you the permission to sell what is made from using the tool. In that case, the patent is designed to stop you using a rival tool with the patented method.

Of course, with a patent like this that only covers a method, it is hard if not impossible to tell from a chip alone whether the method was used. So the patent holder may find it hard to prove infringement. Again the patent is likely on a practical level to be more useful against other parties selling rival tools.

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