test_growth

Perform tests on an instance of cobra.Model using growth data.

Growth data comes from processed biolog experiments. Growth curves have to be converted into binary decisions whether or not an organism/strain was able to grow in a certain medium.

Module Contents

Functions

test_growth_from_data_qualitative(model, experiment, threshold=0.95)

Expect a perfect accuracy when predicting growth.

test_growth.test_growth_from_data_qualitative(model, experiment, threshold=0.95)

Expect a perfect accuracy when predicting growth.

The in-silico growth prediction is compared with experimental data and the accuracy is expected to be better than 0.95. In principal, Matthews’ correlation coefficient is a more comprehensive metric but is a little fragile to not having any false negatives or false positives in the output.

Implementation: Read and validate experimental config file and data tables. Constrain the model with the parameters provided by a user’s definition of the medium, then compute a confusion matrix based on the predicted true, expected true, predicted false and expected false growth. The individual values of the confusion matrix are calculated as described in https://en.wikipedia.org/wiki/Confusion_matrix