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Experts are available at the J.A. Comenius Museum to advise visiting scholars on their research. The museum professionals expertises include Comeniology, theology, regional history, and archaeology. Scholars may consult their questions with custodians of collections who oversee the historical, ethnographical, or art collections (including a section specifically focused on John Amos Comenius), as well as the library containing old prints and maps.
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Relationships with several institutions are established, such as the Institute of Philosophy of the Czech Academy of Sciences, and several state-funded museums in the Czech Republic.
The J.A. Comenius Museum organises international scientific colloquia on Comeniological topics every two years, together with other institutions as the Comenius Museum and Mausoleum in Naarden, the University of Groningen, and the Institute of Philosophy of the Czech Academy of Sciences, Prague.
The museum publishes the journal Studia Comeniana et historica (SCetH), which deals with Comeniology, the history of the 16th to 18th centuries and the regional history of the Moravian-Slovak border region. It has been published continuously since 1971.