The AEI participates in the following European governing bodies:
- GPC-ERAC: High Level Group of the European Research Area (ERA) for the definition of Joint Programming. Created by the European Council and the European Commission. The AEI participates in this group together with the CDTI.
- Joint Programming Group: Created in 2016 on the recommendation of the Spanish roadmap towards the European Research Area (ERA, for its acronym in English). The AEI is coordinated by the Group made up of representatives of the AEI itself, CDTI, ISCIII, INIA, FECYT and with the participation of the Ministry of Science and Innovation.
- JPI WATER: Joint programming initiative related to water research. The AEI participates in the governing council and the executive council. The AEI also coordinates one of the European projects with EU co-financing, WaterWorks 2014.
- JPI OCEANS: Joint programming initiative related to ocean research. AEI participates as an associated country.
- JPI CLIMA: Joint programming initiative related to climate observation. AEI participates as an associated country.
- JPI CULTURAL HERITAGE: Joint programming initiative related to research on European cultural heritage. AEI participates as an associated country.
- JPI HDHL: Joint programming initiative related to diet and healthy living. The AEI participates in its governing bodies together with the ISCIII.
- JPI MYBL: Joint programming initiative related to research on aging. The AEI participates in the governing council together with the ISCIII.
- JPI AMR: Joint programming initiative related to research on antimicrobial resistance. The AEI participates in its governing bodies together with the ISCIII.
- JPND: Joint programming initiative related to research on Alzheimer's and other neurodegenerative diseases. The CDTI participates in its governing bodies together with the ISCIII. The AEI maintains a follow-up position.
- JPI URBAN: Joint programming initiative related to research in the global management of cities, including social and sustainability aspects. The AEI participates as an observer.
- JTI ECSEL-JU: Research joint venture on nano electronics and integrated systems. The AEI participates in the groups of funding agencies and the definition of strategic areas together with the Secretary of State for Digitalization and Artificial Intelligence (SEDIA-MAETD).
In Horizon Europe, the ECSEL baton has been taken over by the new joint venture Key Digital Technologies (KDT JU), under art. 187 of the TFEU. The AEI has participated since 2020 in defining the KDT program together with SEDIA. The AEI will finance the participation of academic entities, while the SEDIA will finance the participation of the private sector. - JTI Euro-HPC-JU: Joint Venture for European High Efficiency Computing. The AEI participates in the governing council together with the MCIN.
The AEI participates in the following governing bodies outside the European sphere:
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CRCNS Program. Collaboration agreement with the United States on computational neuroscience, signed by the National Science Foundation (NSF), the National Institutes of Health (NIH) and the Department of Energy (DOE) of the United States and by the State Research Agency and the Institute of Salud Carlos III, on the part of Spain. In 2018, the AEI and the Carlos III Health Institute signed a tripartite collaboration agreement with the US National Science Foundation (NSF) that gave access to the CRCNS program. This is a very competitive program in which only four countries participate, in addition to Spain and the US: Japan, France, Germany and Israel.
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CYTED. Science and Technology for Development Program, created by the governments of the Ibero-American countries to promote cooperation in science, technology and innovation issues for the harmonious development of Ibero-America.
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EU-CELAC Interest Group. Composed of 28 funding agencies from Latin America, the Caribbean and Europe that wish to collaborate in bi-regional science, technology and innovation (CTI), and the implementation of the EU-CELAC Common Research Space through joint actions.
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European Interest Group (EIG) Concert Japan. It is an international joint initiative to support and improve cooperation in science, technology and innovation (CTI) between European countries and Japan.