Abstract: Systems and methods for implementing one or more compiled workflows at a biological foundry are provided. A representation of an uncompiled workflow to produce engineering targets is obtained. The representation is translated into a first corresponding instance of a compiled workflow. If the translation satisfaction of various threshold translation criteria is determined, and the first corresponding instance of the compiled workflow is executed to complete a first portion of manufacture of the engineering targets. If the executing satisfaction of various threshold execution criteria is determined, the representation is translated into a second corresponding instance of the compiled workflow different from the first corresponding instance. If this translation satisfaction of the various threshold translation criteria is determined, the second corresponding instance of the compiled workflow is executed to complete a second portion of the manufacture of the engineering targets.