  We study the coherent flow of a guided Bose-Einstein condensate incident over
a disordered region of length L. We introduce a model of disordered potential
that originates from magnetic fluctuations inherent to microfabricated guides.
This model allows for analytical and numerical studies of realistic transport
experiments. The repulsive interaction among the condensate atoms in the beam
induces different transport regimes. Below some critical interaction (or for
sufficiently small L) a stationary flow is observed. In this regime, the
transmission decreases exponentially with L. For strong interaction (or large
L), the system displays a transition towards a time dependent flow with an
algebraic decay of the time averaged transmission.
