  Engineering the entire genome of an organism enables large-scale changes in
organization, function, and external interactions, with significant
implications for industry, medicine, and the environment. Improvements to DNA
synthesis and organism engineering are already enabling substantial changes to
organisms with megabase genomes, such as Escherichia coli and Saccharomyces
cerevisiae. Simultaneously, recent advances in genome-scale modeling are
increasingly informing the design of metabolic networks. However, major
challenges remain for integrating these and other relevant technologies into
workflows that can scale to the engineering of gigabase genomes.
  In particular, we find that a major under-recognized challenge is
coordinating the flow of models, designs, constructs, and measurements across
the large teams and complex technological systems that will likely be required
for gigabase genome engineering. We recommend that the community address these
challenges by 1) adopting and extending existing standards and technologies for
representing and exchanging information at the gigabase genomic scale, 2)
developing new technologies to address major open questions around data
curation and quality control, 3) conducting fundamental research on the
integration of modeling and design at the genomic scale, and 4) developing new
legal and contractual infrastructure to better enable collaboration across
multiple institutions.
