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The Project provides an upgrading of the commuter rail system in Istanbul, connecting Halkalı on the European side with Gebze on the Asian side with an uninterrupted, modern, high-capacity commuter rail system.

Railway tracks in both sides of Istanbul Strait will be connected to each other through a railway tunnel connection under the Istanbul Strait. The line goes underground at Yedikule, continues through the Yenikapı and Sirkeci new underground stations, passes under the Istanbul Strait, connects to the Üsküdar new underground station and emerges at Sögütlüçesme.

This Project is one of the major transportation infrastructure projects in the world at present. The entire upgraded and new railway system will be approximately 76 km long. The main structures and systems; include the immersed tube tunnel, bored tunnels, cut-and-cover tunnels, at - grade structures, three new underground stations, 37 surface stations (renovation and upgrading), operations control centre, yards, workshops, maintenance facilities, upgrading of existing tracks including a new third track on ground, completely new electrical and mechanical systems and procurement of modern railway vehicles.

The idea of a railway tunnel under the Istanbul Strait was first raised in 1860. However, where the tunnel under the Istanbul Strait crosses the deepest parts of the Strait, the old-fashioned techniques would not allow the tunnel to be on or under the seabed, and therefore the design indicated a "floating" type of tunnel placed on pillars constructed on the seabed.

Such ideas developed further during the following decades, and a similar design was developed in 1902 also showing a railway tunnel under the Istanbul Strait, but this design indicates a tunnel placed on the seabed. Since then, several different ideas have been tested and new technologies have allowed more freedom in the design.

The technique that will be used in the Marmaray Project to cross the Istanbul Strait - the immersed tube tunnel technique - has been developed since late in the 19th century. The first immersed tube tunnel ever built was constructed in North America for sewer purposes in 1894. The first tunnels for traffic purposes constructed using this technique were also built in the United States. The first one was the Michigan Central Railroad tunnel in 1906-1910. In Europe, Holland was the first country to adopt the technique, and the Maas Tunnel in Rotterdam was opened in 1942. . In Asia, Japan was the first country to adopt this techniques and the two-tube road tunnel (Aji River Tunnel) in Osaka was opened in 1944. However, such tunnels remained rare until a robust and well proven industrial technique was developed in the 1950s, thereby allowing the construction of large-scale projects in many countries.

The desire to construct a railway mass transit connection from west to east in Istanbul and under the Istanbul Strait was becoming stronger and stronger in the early 1980s, and consequently the first comprehensive feasibility study was carried out and reported in 1987. This study concluded that such a connection would be feasible and cost-effective, and the alignment we see in the project today was selected as the best of a range of alignments.

The project as outlined in 1987 was discussed during the following years, and around 1995 it was decided to make more detailed studies and update the feasibility studies, including the passenger demand forecast from 1987. These studies were concluded in 1998, and the conclusions underlined the earlier conclusions that the project would offer many advantages to the people working and living in Istanbul, and it would ease the rapidly growing problems regarding traffic congestion in the city.

In 1999, a funding agreement between the Republic of Turkey and the Japanese Bank for International Cooperation (JBIC) was signed. This loan agreement forms the basis for the funding of the Istanbul Strait Crossing portion of the Project, which represents some 35% of the costs for the entire railway project