Scalable experimental workflow for parameter estimation

A computer-implemented method comprising:

• determining, for a culture system, a dilution cycle with a predetermined period and a desired optical density;
• measuring, for the dilution cycle, an actual optical density of a culture chamber of the culture system;
• determining, for the culture chamber, a dilution rate as a function between the desired optical density and the actual optical density;
• controlling a pump, a valve, or a combination thereof to provide fresh medium to the culture chamber at the dilution rate to return a turbidity of a biological system to the desired optical density;
• measuring, by an analyzer, a characteristic of one or more characteristics in a sample of the biological system from the culture chamber to obtain at least a portion of measurement data;
• obtaining the measurement data for the one or more characteristics of the biological system developed in the culture system, wherein the measurement data is indicative of each of the one or more characteristics at a physiological steady state where growth of the biological system is occurring at a substantially constant growth rate, and wherein the obtaining the measurement data comprises retrieving the portion of the measurement data from the analyzer;
• determining a value for a parameter of a model of the biological system based on a growth formula, the measurement data, and the substantially constant growth rate, wherein the model predicts a response of the biological system to a set of conditions based on a plurality of parameters including the parameter, and the parameter models an aspect of structure or function of the biological system;
• and
• parametrizing the model with at least the value determined for the parameter.

A computer-program product tangibly embodied in a non-transitory machine-readable storage medium, including instructions configured to cause one or more data processors to perform actions including:

• determining, for a culture system, a dilution cycle with a predetermined period and a desired optical density;
• measuring, for the dilution cycle, an actual optical density of a culture chamber of the culture system;
• determining, for the culture chamber, a dilution rate as a function between the desired optical density and the actual optical density;
• controlling a pump, a valve, or a combination thereof to provide fresh medium to the culture chamber at the dilution rate to return a turbidity of a biological system to the desired optical density;
• measuring, by an analyzer, a characteristic of one or more characteristics in a sample of the biological system from the culture chamber to obtain at least a portion of measurement data;
• obtaining the measurement data for the one or more characteristics of the biological system developed in the culture system, wherein the measurement data is indicative of each of the one or more characteristics at a physiological steady state where growth of the biological system is occurring at a substantially constant growth rate, and wherein the obtaining the measurement data comprises retrieving the portion of the measurement data from the analyzer;
• determining a value for a parameter of a model of the biological system based on a growth formula, the measurement data, and the substantially constant growth rate, wherein the model predicts a response of the biological system to a set of conditions based on a plurality of parameters including the parameter, and the parameter models an aspect of structure or function of the biological system;
• and
• parametrizing the model with at least the value determined for the parameter.