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The Matrix is a gigantic facility used to produce and bring life to Maximal protoforms. Apparently it is named after the Creation Matrix. Both the Matrix and the Pit are located in an isolated area on Cybertron. The Matrix and Pit are capable of self-defense, making themselves veritable fortresses. Nobody knows when the facilities first appeared on the planet. The Matrix periodically rolls out Maximal protoforms. 
Timelines: The Razor's Edge
The Matrix facility, like its twin Pit, originated in pseudocanonical sources and the vast majority of what we know about it remains pseudocanon. The statements in the fiction section -- derived from exactly two sentences of The Razor's Edge constitute the whole of canonical information on these facilities.
The idea of the Matrix and Pit facilities was introduced to the fandom through Bob Forward and Larry DiTillio's posts to the newsgroup alt.toys.transformers during the years that Beast Wars was airing on North American television. Bob'n'Larry had seemingly not fully formed the idea behind the facilities at the time that they mentioned them on ATT. Years later, DiTillio provided some background information for a Japanese guidebook called Beast Wars Universe including some additional information about the facilities. Here DiTillio states that the Allspark dimension (aka the Matrix dimension) is the same thing as the Vok Nebula, the "cloud" that the Vok are shown inhabiting (also sometimes referred to as Nexus Zero). Again according to this interview, the Vok created protoforms and they presumably are the ones responsible for mysteriously plopping the Matrix and Pit down on Cybertron.
It should be emphasized that none of this information is present in any actual Transformers fiction, and is barely even suggested by any fiction, although it is possible to incorporate the information fairly smoothly. The Razor's Edge is the first -- and so far only -- fiction to say anything specific about the facilities.