Whats a protocol?
A protocol is an ordered set of Scriptome atoms which can solve a larger problem. The analogy is to a biological protocol (such as those at http://www.genome.ou.edu/protocol_book/protocol_index.html), which is an ordered set of actions that solve a larger biological problem. Protocols can be found in the Protocols section of the navigation bar on the left, although users will often want to build their own protocols.
