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We consider a class of super-conformal beta-deformed N=1 gauge theories dual to string theory on with fluxes, where is a deformed Sasaki-Einstein manifold. The supergravity backgrounds are explicit examples of Generalised Calabi-Yau manifolds: the cone over admits an integrable generalised complex structure in terms of which the BPS sector of the gauge theory can be described. The moduli spaces of the deformed toric N=1 gauge theories are studied on a number of examples and are in agreement with the moduli spaces of D3 and D5 static and dual giant probes.

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