Simulating the metabolic pathway dynamics of an organism

A system for simulating the pathway dynamics of a virtual strain of an organism, comprising:

• computer-readable memory storing executable instructions;
• and
• one or more hardware processors programmed by the executable instructions to perform a method comprising:
• receiving time-series multiomics data of a plurality of strains of the organism, the times-series multiomics data comprising time-series metabolomics data and time-series proteomics data associated with a metabolic pathway;
• determining derivatives of the time-series metabolomics data;
• training a machine learning model, representing a metabolic pathway dynamics model, using the time-series multiomics data and the derivatives of the time-series metabolomics data, wherein the metabolic pathway dynamics model relates the time-series metabolomics data and time-series proteomics data to the derivatives of the time-series metabolomics data;
• and
• simulating a virtual strain of the organism using the metabolic pathway dynamics model to determine a characteristics of a metabolic pathway represented by the metabolic pathway dynamics model in the virtual strain.