Massachusetts Bay Transportation Authority
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Artikel utama: MBTA subway
The subway system has three heavy rail rapid transit lines (the Red, Orange and Blue Lines), and two light rail lines (the Green Line and the Ashmont–Mattapan High-Speed Line, the latter designated an extension of the Red Line). The system operates according to a spoke-hub distribution paradigm, with the lines running radially between central Boston and its environs. It is common usage in Boston to refer to all four of the color-coded rail lines which run underground as "the subway" or "the T", regardless of the actual railcar equipment used.
All four subway lines cross downtown, forming a quadrilateral configuration, and the Orange and Green Lines (which run approximately parallel in that district) also connect directly at two stations just north of downtown. The Red Line and Blue Line are the only pair of subway lines which do not have a direct transfer connection to each other. Because the various subway lines do not consistently run in any given compass direction, it is customary to refer to line directions as "inbound" or "outbound".  Inbound trains travel towards the four downtown transfer stations, and outbound trains travel away from these hub stations.
The Green Line has four branches in the west: B (Boston College), C (Cleveland Circle), D (Riverside), and E (Heath Street). The A branch formerly went to Watertown, filling in the north-to-south letter assignment pattern, and the E branch formerly continued beyond Heath Street to Arborway.
The Red Line has two branches in the south, Ashmont and Braintree, named after their terminal stations.
The colors were assigned on August 26, 1965 in conjunction with design standards developed by Cambridge Seven Associates, and have served as the primary identifier for the lines since the 1964 reorganization of the MTA into the MBTA. The Orange Line is so named because it used to run along Orange Street (now lower Washington Street), as the former "Orange Street" also was the street that joined the city to the mainland through Boston Neck in colonial times; the Green Line because it runs adjacent to parts of the Emerald Necklace park system; the Blue Line because it runs under Boston Harbor; and the Red Line because its northernmost station was, at that time, at Harvard University, whose school color is crimson.
The four transit lines all use standard rail gauge, but are otherwise incompatible; trains of one line would have to be modified to run on another. Orange and Blue Line trains are similar enough that modification of some Blue Line trains for operation on the Orange Line was considered, although ultimately rejected for cost reasons. Also, some of the new Blue Line cars from Siemens Transportation were tested on the Orange Line after hours, before acceptance for revenue service on the Blue Line. There are no direct track connections between lines, except between the Red Line and Ashmont-Mattapan High Speed Line, but all except the Blue Line have little-used connections to the national rail network, which have been used for deliveries of railcars and supplies.
Opened in September 1897, the four-track-wide segment of the Green Line tunnel between Park Street and Boylston stations was the first subway in the United States, and has been designated a National Historic Landmark. The downtown portions of what are now the Green, Orange, Blue, and Red line tunnels were all in service by 1912. Additions to the rapid transit network occurred in most decades of the 1900s, and continue in the 2000s with the addition of Silver Line bus rapid transit and planned Green Line expansion. (See History and Future plans sections.)
In FY2005, there were on average 628,400 weekday boardings on the rapid transit and light rail lines (including the Silver Line Bus Rapid Transit), or 55.0% of the MBTA system.
On January 29, 2014, the MBTA completed a countdown clock display system, alerting passengers to arriving trains, at all 53 heavy rail subway stations (the Red, Blue and Orange Lines). The MBTA introduced countdown clocks in underground Green Line stations during 2015. Unlike the other countdown clocks which count down in minutes, the Green Line clocks count down the number of stops away the train is.