It is often discussed that the fourth methodology for science research is "informatics". The first methodology is a theoretic approach, the second one is observation and/or experiment, and the third one is computer simulation. Informatics is a new methodology for data intensive science, which is a new concept based on the fact that most scientific data are digitalized and the amount of data is huge. The facilities to support informatics are cloud systems. Herein we propose a cloud system especially designed for science. The basic concepts, design, resources, implementation, and applications of the NICT science cloud are discussed.