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The second thing to remember is that you should get a contactless prepaied electronic card ticket like the London's "Oyster card" for public transport : "Suica", "Pasmo", "Icoca" etc. The function is all the same, the names of the cards just depend on the issuing organizations. Please note that all the vending machines only accept Japanese notes (some of them accept Japanese coins). "Suica" has the smartphone application and its English version "SuicaEng".
They are valid within all the metropolitan areas each other, but impossible to cross the areas. With "Japan Rail Pass", which is equivalent to the 'Eurail Pass' and the 'BritRail Pass', you can travel allover Japan using JR (ex-Japan National Railways) lines including "Shinkansen" super bullet express but this stingy pass is not valid for the quickest and most frequent (almost every 5 min.) Shinkansen 'Nozomi (=hope)' but only for 'Hikari (=light)' and 'Kodama (=echo)', both of which only run twice an hour.
Something is not right. This message is just to keep things from messing up down the road