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Japan Science and Technology Agency was formed by merging two existing organizations: Japan Information Center of Science and Technology (JICST) and Research Development Corporation of Japan (JRDC). JICST was founded in August 1957 as a Japan's core institution for science and technology information, with a view to providing the Japanese public with both national and international information on science and technology in a prompt and accurate manner. Meanwhile, JRDC was organized in July 1961 with missions to reduce the country's dependence on overseas technologies, to select and support outstanding research at universities and public research institutions in Japan, and to promote technology transfer of such research output to the private sector.
In October 1996, JICST and JRDC were merged into Japan Science and Technology Corporation (JST) aiming at both strengthening the infrastructure for the promotion of science and technology in a comprehensive and efficient way, as well as vigorously implementing initiatives set out in the Science and Technology Basic Law. In October 2003, the former JST was reorganized as an independent administrative institution, Japan Science and Technology Agency (JST).

The ellipse surrounding the letters 'JST' and the red dot above it calls to mind an image of the earth and the solar system from a macro perspective, as well as an electron and its nucleus from a micro perspective. JST is located at the core here, symbolizing JST's ceaseless efforts to promote science and technology from every perspective from the micro to macro. Also, at the same time, just as the morning sun rises naturally, the red dot represents JST's stance of continued future-oriented growth, onward and upward.