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Trains are the major means of transportation in Japan. Transit network systems in city areas are complex but very efficient and punctual. During commuting hours, trains are extremely crowded especially in metropolitan areas.
Fares generally depend on how far you travel. You must purchase a ticket at a ticket vending machine before you ride the train. If you are a frequent train user, you might want to purchase a prepaid electronic pass, Suica or PASMO, which saves you the trouble of buying a ticket every time you travel. With these passes, you can go through ticket gates by simply holding your card over the scanner. For details about Suica and PASMO, see their respective websites.
If you are a degree-seeking student (either undergraduate or graduate student) and use trains to commute, you are eligible to apply for the student discount commuting pass (Teiki-ken) .
The bus transportation network is also quite extensive in city areas and very punctual. Each bus stop has a unique name, usually named after the area or a nearby landmark. On the bus, an announcement will tell you the next bus stop. The fare can be paid using Suica or PASMO for most bus services in city areas; the fare is paid before or after riding, depending on the route.
Shinkansen is a long-distance transportation train offered by Japan Railways (JR) and is known for its high speed, style, service, and punctuality. Many tour packages visiting famous cities and historic places throughout Japan by Shinkansen are offered at relatively low fares. For more information, refer to the following website.
Flying is another way to travel within Japan, especially to other islands. Besides the major airline companies, All Nippon Airways (ANA) and Japan Airlines (JAL), low cost carriers (LCC) are on the rise in Japan.