The objective of this study was to develop an approach for translation of cognitive task analysis (CTA) results to training program content for operators of high throughput screening (HTS) systems. Currently, no standardized methods exist for translating outcomes of multiple CTA methods to support training program design and promote situation awareness (SA). We combined information requirements from a goal-directed task analysis (GDTA) and system resource requirements from abstraction hierarchy (AH) models to establish content on HTS processes and to address three levels of operator SA. The two electronic forms of training were compared with on-the-job (OTJ) training. Results provided preliminary evidence that CTA-based training increased operator knowledge beyond OTJ training and increased SA-related knowledge beyond operator initial system knowledge. A set of general guidelines was developed for design of CTA-based training programs, including methods for structuring components of the training program to support SA.