Abstract: A microorganism engineering project employs a vector representation of a biological network. The vector representation allows researchers to input elements known to have a direct impact on a goal of the project (e.g., an element in the metabolic pathway for generating a compound of interest). Within the vector representation, other biological elements are positioned with respect to an input element based on biological relatedness. In this manner, based on positions within the vector representation, candidate elements may be identified for editing. For example, if the elements are associated with a gene, the gene sequence may be knocked out and/or a different promoter may be used for regulating the gene.

Abstract: Systems, methods and computer-readable media are provided for designing experiments for organisms at a first scale to generate first-scale performance data used in predicting performance of the organisms at a second, larger scale. The design includes determining first-scale screening conditions based at least in part upon the contribution of second-scale conditions to performance parameters of an organism at the second scale. The first-scale screening conditions include one or more proxies for second-scale conditions that cannot be replicated at first scale. The design determines first-scale screening parameters based at least in part upon computer modeling of the metabolism of the organism at the second scale.

Abstract: Systems, methods and computer-readable media storing executable instructions are provided for improving performance of an organism with respect to a phenotype of interest at a second scale based upon measurements at a first scale. First scale performance data based at least in part upon observed first performance of first organisms at a first scale and second scale performance data based at least in part upon observed second performance of second organisms at a second scale larger than the first scale are accessed. A prediction function based at least in part upon the relationship of the second scale performance data to the first scale performance data is generated. The prediction function may be applied to performance data observed for test organisms with respect to the phenotype of interest at the first scale to generate second scale predicted performance data for the test organisms at the second scale.