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Since January 2011, CECT has been located on the ground floor of Building 3 CUE at the Scientific Park of the University of Valencia, in Paterna, 10 km from Valencia, occupying an area of ​​approximately 677 m2.

To comply with biosecurity regulations for Microbial Resource Centers, it has two separate wings, one with restricted access for CECT staff and another with open access. In the restricted access wing, there is the office of the microbial responsible personnel, two laboratories (one for Prokaryotes - bacteria and archaea - and another for Eukaryotes - filamentous fungi and yeasts), three rooms (cleaning of materials, preparation of culture media, sterilization, and lyophilization), four cold rooms (for the conservation of culture media, maintenance of strains not resistant to lyophilization or freezing, maintenance of samples received for deposition or identification, and long-term conservation of microorganisms - lyophilized or in liquid nitrogen), and a refrigerated room housing -80°C freezers, as a complementary/alternative method for microorganism conservation, a climatic chamber, and part of CECT's servers. In the open access wing, there are several offices (management, administration, order reception, research personnel, etc.), three specialized laboratories (chemotaxonomy, molecular techniques, a general microbiology laboratory for training and short stays of guest researchers), and two storage spaces.

The most effective method for long-term conservation of microorganisms is lyophilization, so most strains in the collection are maintained lyophilized in glass ampoules, protected from light in opaque black plastic bags, in a climatic chamber at 10°C. However, some microbial groups, such as certain genera of filamentous fungi, do not withstand this method, so it is necessary to keep them active through periodic reseeding and storage at 4°C. All strains are also maintained at -80°C. Additionally, a duplicate of the collection is kept in lyophilized format at the Jeroni Muñoz Building (approximately 1 kilometer away) in compliance with Good Practices for Microbial Resource Centers.

Regarding computer equipment, CECT maintains several servers, which host the strain database and the public catalog, email, and the shared file storage system. It also has a molecular biology server, from which various sequence manipulation and alignment programs or other data are accessible. To ensure data integrity, CECT performs remote backups of all its servers.