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The FBI is headquartered at the J. Edgar Hoover Building in Washington, D.C., with 56 field offices in major cities across the United States. The FBI also maintains over 400 resident agencies across the United States, as well as over 50 legal attachés at United States embassies and consulates. Many specialized FBI functions are located at facilities in Quantico, Virginia, as well as a "data campus" in Clarksburg, West Virginia, where 96 million sets of fingerprints "from across the United States are stored, along with others collected by American authorities from prisoners in Saudi Arabia and Yemen, Iraq and Afghanistan." The FBI is in process of moving its Records Management Division, which processes Freedom of Information Act (FOIA) requests, to Winchester, Virginia.

According to The Washington Post, the FBI "is building a vast repository controlled by people who work in a top-secret vault on the fourth floor of the J. Edgar Hoover Building in Washington. This one stores the profiles of tens of thousands of Americans and legal residents who are not accused of any crime. What they have done is appear to be acting suspiciously to a town sheriff, a traffic cop or even a neighbor."

The FBI Laboratory, established with the formation of the BOI, did not appear in the J. Edgar Hoover Building until its completion in 1974. The lab serves as the primary lab for most DNA, biological, and physical work. Public tours of FBI headquarters ran through the FBI laboratory workspace before the move to the J. Edgar Hoover Building. The services the lab conducts include Chemistry, Combined DNA Index System (CODIS), Computer Analysis and Response, DNA Analysis, Evidence Response, Explosives, Firearms and Tool marks, Forensic Audio, Forensic Video, Image Analysis, Forensic Science Research, Forensic Science Training, Hazardous Materials Response, Investigative and Prospective Graphics, Latent Prints, Materials Analysis, Questioned Documents, Racketeering Records, Special Photographic Analysis, Structural Design, and Trace Evidence. The services of the FBI Laboratory are used by many state, local, and international agencies free of charge. The lab also maintains a second lab at the FBI Academy.

The FBI Academy, located in Quantico, Virginia, is home to the communications and computer laboratory the FBI utilizes. It is also where new agents are sent for training to become FBI Special Agents. Going through the 21-week course is required for every Special Agent. First opened for use in 1972, the facility located on 385 acres (1.6 km2) of woodland. The Academy trains state and local law enforcement agencies, which are invited to the law enforcement training center. The FBI units that reside at Quantico are the Field and Police Training Unit, Firearms Training Unit, Forensic Science Research and Training Center, Technology Services Unit (TSU), Investigative Training Unit, Law Enforcement Communication Unit, Leadership and Management Science Units (LSMU), Physical Training Unit, New Agents' Training Unit (NATU), Practical Applications Unit (PAU), the Investigative Computer Training Unit and the "College of Analytical Studies."

In 2000, the FBI began the Trilogy project to upgrade its outdated information technology (IT) infrastructure. This project, originally scheduled to take three years and cost around $380 million, ended up over budget and behind schedule. Efforts to deploy modern computers and networking equipment were generally successful, but attempts to develop new investigation software, outsourced to Science Applications International Corporation (SAIC), were not. Virtual Case File, or VCF, as the software was known, was plagued by poorly defined goals, and repeated changes in management. In January 2005, more than two years after the software was originally planned for completion, the FBI officially abandoned the project. At least $100 million (and much more by some estimates) was spent on the project, which never became operational. The FBI has been forced to continue using its decade-old Automated Case Support system, which IT experts consider woefully inadequate. In March 2005, the FBI announced it was beginning a new, more ambitious software project, code-named Sentinel, which they expected to complete by 2009.

Carnivore was an electronic eavesdropping software system implemented by the FBI during the Clinton administration; it was designed to monitor email and electronic communications. After prolonged negative coverage in the press, the FBI changed the name of its system from "Carnivore" to "DCS1000." DCS is reported to stand for "Digital Collection System"; the system has the same functions as before. The Associated Press reported in mid-January 2005 that the FBI essentially abandoned the use of Carnivore in 2001, in favor of commercially available software, such as NarusInsight.

The Criminal Justice Information Services (CJIS) Division is located in Clarksburg, West Virginia. Organized beginning in 1991, the office opened in 1995 as the youngest agency division. The complex is the length of three football fields. It provides a main repository for information in various data systems. Under the roof of the CJIS are the programs for the National Crime Information Center (NCIC), Uniform Crime Reporting (UCR), Fingerprint Identification, Integrated Automated Fingerprint Identification System (IAFIS), NCIC 2000, and the National Incident-Based Reporting System (NIBRS). Many state and local agencies use these data systems as a source for their own investigations and contribute to the database using secure communications. FBI provides these tools of sophisticated identification and information services to local, state, federal, and international law enforcement agencies.

FBI is in charge of National Virtual Translation Center, which provides "timely and accurate translations of foreign intelligence for all elements of the Intelligence Community."

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