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The San Francisco Plague Commission series is a small grouping of materials from the period in 1901 when Novy as part of a commission was investigating the possibility of bubonic plague in this California city. This series includes a scrapbook of clippings from San Francisco newspapers, notes from cases of plague, testimony, a copy of the report, and scattered correspondence and other documents. Novy's impressions of his work and his life in the city will be found in his letters to his wife in the Correspondence series.

The Research Files/Laboratory Notebooks series includes approximately fifty laboratory notebooks documenting experiments and other research done by Novy, as well as various notes on research projects.