System and method for prediction of unintended gene expression impact in a fermentation process

A system for selecting an engineered organism with a desired protein expression, the system comprising:

• at least one memory storing instructions;
• and
• at least one processor communicatively coupled to the at least one memory and configured to perform operations comprising:
• receiving a request for a desired composition profile produced from a mixture;
• analyzing the mixture to determine a respective quantity of a plurality of different compounds in the mixture;
• selecting a gene of a yeast to interact with one or more of the compounds;
• creating a plurality of gene editions based on the gene;
• simulating expression of the plurality of gene editions to determine impact on the gene and a plurality of other genes;
• selecting, from the plurality of gene editions, a plurality of designated gene editions that satisfy at least one predetermined criteria;
• simulating a reaction with the mixture and the yeast having individual ones of the plurality of designated gene editions, wherein the simulating includes a plurality of hours, the mixture, and the yeast having the individual ones of the plurality of designated gene editions;
• determining an expected final composition after a plurality of the simulated reactions;
• correlating data on a plurality of attributes of the expected final compositions to the desired final composition profile;
• selecting one or more expected final compositions that most closely match the desired composition profile;
• and
• providing related gene edition data that produced the selected one or more expected final compositions.

A non-transitory computer-readable media comprising instructions stored thereon, which, when executed by at least one processor of at least one computing device for selecting an engineered organism with a desired protein expression, cause the at least one computing device to perform operations comprising:

• receiving a request for a desired composition profile produced from a mixture;
• analyzing the mixture to determine a respective quantity of a plurality of different compounds in the mixture;
• selecting a gene of a yeast to interact with one or more of the compounds;
• creating a plurality of gene editions based on the gene;
• simulating expression of the plurality of gene editions to determine impact on the gene and a plurality of other genes;
• selecting, from the plurality of gene editions, a plurality of designated gene editions that satisfy at least one predetermined criteria;
• simulating a reaction with the mixture and the yeast having individual ones of the plurality of designated gene editions, wherein the simulating includes a plurality of hours, the mixture, and the yeast having the individual ones of the plurality of designated gene editions;
• determining an expected final composition after a plurality of the simulated reactions;
• correlating data on a plurality of attributes of the expected final compositions to the desired final composition profile;
• selecting one or more expected final compositions that most closely match the desired composition profile;
• and
• providing related gene edition data that produced the selected one or more expected final compositions.