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In 1711–1717, Stepan Malygin was a student at the Moscow School of Mathematical and Navigational Sciences. After his graduation, Malygin began his career as a naval cadet and was then promoted to the rank of lieutenant four years later. He served in the Baltic Fleet until 1735.
Stepan Malygin was the first one to write a Russian manual on navigation called Сокращённая навигация по карте де-Редукцион (1733). In the early 1736, Malygin was appointed leader of the western unit of the Second Kamchatka Expedition. In 1736–1737, two boats Perviy (First) and Vtoroy (Second) under the command of Stepan Malygin and A.Skuratov undertook a voyage from the Dolgiy Island in the Barents Sea to the mouth of the Ob River. During this trip, Malygin described this part of the Russian Arctic coastline and made a map of the area between the Pechora and Ob Rivers.