Integration and holes in the BioCAD toolchain

The automation of DNA fabrication and strain characterization is ushering in a new era to metabolic engineering.  Where once it was prohibitively costly to test many designs during a project, automated fabs can now prototype strains and test them on a massive scale. This scaling in our ability to experimentally survey the design space moves the bottleneck in identifying new and useful organisms from physical experiments to issues of target selection, strain design, cost analysis, biosafety, intellectual property, and regulatory concerns. It also raises the more general problems of how these tools get integrated into a coherent environment, how the large amount of new knowledge is distributed, how it is attributed, and the mechanisms for training in the use of this new infrastructure. I will provide an overview of the tools that currently exist, the holes that remain, and the Clotho platform for integration.