Organism engineering is a field that employs principles of genetic engineering, synthetic biology, and bio-manufacturing to rapidly test and produce new genetically modified organisms at very large scales. Automation systems are often employed at these large scales to manage and execute laboratory operations. A current challenge in the field is how to automate organism engineering during the discovery phase of research when experimental failure rates are high and laboratory methodologies are variable. Here we demonstrate progress towards creating automated systems for rapidly engineering new strains of S. cerevisiae, or baker’s yeast, during the discovery phase of research. This dissertation details (i) the design and construction of a new set of CRISPR-based genetic parts that can be used to engineer new behaviors in yeast, (ii) accompanying lab software that can be used to automate the engineering of new yeast strains, and (iii) applications of lab automation software to global health.