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The monography sets out the tasks of managing scientific research, as well as the problems of the methodology of scientific cognition, including the classification of means and methods that are specific to science and distinguish it from other ways of cognizing, realizing the real world, in addition the basic methods of empirical and theoretical research that characteristic of various stages of the process of scientific. Methods of analysis of existing knowledge and methods of scientific research, which are of greatest interest to future researchers, are considered in detail. Unlike the general cognitive theory, the main attention here is paid to the analysis of those receptions, means and methods of cognition, with the help of which new knowledge is acquired in science. Analysis of the scheduling problem and organization of scientific research and innovation activities is carried out mainly on the basis of natural science knowledge, although many conclusions are applicable to the cognition of social phenomena. The monography is intended for students, undergraduates and doctoral students of PhD, as well as for researchers involved in the management of research and innovation.