A number of computational tools have been developed for composing synthetic gene circuits, managing workflows, and simulating their behavior. Less attention has been directed towards the underlying parts that go into these designs. New computational approaches nonetheless are being developed for engineering these parts and relating their underlying DNA or amino-acid sequences to functional parameters. These approaches range from detailed mechanistic models to simple ones based on statistical correlations. The challenges will be to integrate the disparate tools into a common framework for the computer-aided design of synthetic gene circuits. ► A number of computational tools have been developed for synthetic biology. ► This manuscript reviews the computational tools for the design of genetic parts in bacteria. ► Integrating these tools into common framework is still an open challenge.
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