Scientists currently enjoy unprecedented access to custom genetic constructs through synthetic biology. The cost of gene synthesis falls while efficiency rises – circumstances that have encouraged researchers to move beyond gene and pathway synthesis towards whole genome synthesis. A chemically synthesized genome has the benefit of being customizable, offering designers a chance to test otherwise intractable hypotheses about chromosome structure, function, and evolution. However, while tools for the design of synthetic genes abound, the larger-scale problem of computer-assisted chromosome design remains unaddressed. Practitioners currently either edit sequence by hand or press smaller design tools into awkward service. An optimal genome design framework allows a team of designers to make coordinated modifications to sequence at both the base pair and the genome scale, to track changes, and to roll back changes at multiple scales. These requirements led us to develop BioStudio (BioStudio Browser), an open source framework for genome design.