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St. Mary's College was founded in 2008, as a collaborative effort between the South Sudanese Ministry of Gender, Social Welfare and Religious Affairs and the Roman Catholic Archdiocese of Juba, with the cooperation of the Volunteers' Organization for International Co-operation OVCI la Nostra Famiglia www.ovci.org (INGO which has been continuously working in South Sudan since 1983). Enrollment is open to all eligible citizens of South Sudan. The Vice Chancellor of the university is Paulino Lukudu Loro, the Roman Catholic Archbishop of Juba.

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