Here is a very nice presentation on making tools to help us think.
The speaker claims writing was the first such tool, as it allowed to put thought processes down and study thought itself.
The mathematical notation we use today is another such tool, and is considered the beginning of modern mathematics. It is amazing to think that the birth of modern mathematics is not attributed to a concept but a user interphase.
He presented such tools running on a computer. They basically try to combine three ways of thinking:
Interactive - like playing with models of molecules to understand the structure of complex organic molecules
Visual - like statistical visualisation
Symbolic - writing, raw thought.
Very interesting and well presented.