The Softwire: Virus on Orbis 1 by PJ Haarsma

From the back of the book:
When the children on the seed ship Renaissance are orphaned in outer space, thirteen-year-old Johnny Turnbull and his sister, Ketheria, are forced to work as knud-nits on the Rings of Orbis. But Johnny soon discovers that his is the first human Softwire - he has a special gift that allows him to enter any computer with his mind. And when the central computer on Orbis mysteriously malfunctions, the Citizens point their fingers at the Softwire.