In To This Distant Shore

Sheldon Silva, eccentric computerguru and amateur radio astronomer, accidentally receives and records an unknown signal. He performs his own analysis on the data and makes some small progress in discovering its nature. When the signal is determined to be extraterrestrial, Silva is recruited to participate in an effort to understand it and respond.

However, the signal is not merely a message from another intelligence, it IS another intelligence — an alien mind deconstructed down to the atom and modeled to yield an encoded data set and software which, when reconstituted on our computer systems, became sentient. Although able to instantiate itself, it analyzed our technology as insufficient for its needs until it finds the SSC.

Once the intelligence found the cyclotron, it began to reprogram and reconfigure it for an unknown purpose.