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The development of Qiqqa began in Cambridge, UK, in December 2009. A public alpha was released in April 2010, offering PDF management and brainstorming capabilities. Subsequent releases have seen the incorporation of the Web Library, OCR, integration with BibTeX and other reference managers, and the use of natural language processing (NLP) techniques to guide researchers in their reading.
In 2011, Qiqqa won both the University of Cambridge CUE and CUTEC, and the Cambridge Wireless Discovering Start-Ups competitions. Qiqqa was an award winner in the 2012 Santander Universities Entrepreneurship Awards.
In 2020, Qiqqa decided to change software pricing model and make it free and open-source: "After 10 years of your support we have decided to make Qiqqa open source so that it can be grown and extended by its community of thousands of active users."