Many methods can be used to validate the model’s proposed predictions; however, comparison of in silico predictions with in vivo experiments is a key method for validation. Measuring experimental growth phenotypes at specific conditions can validate the predicted growth under the same conditions. An alternative validation approach is to carry out in silico and in vivo gene deletion experiments (or to compare in silico results with available gene deletion literature) to check whether there is an agreement between model predictions and the actual deletion mutant phenotype. Moreover, omics data from transcriptomics, metabolomics, and pro- teomics experiments can be used to check the consistency of the model’s predicted results. Available simulation debugging tools may be used if the model has poor agreement with experimental data. Further refinement of the model can be done as described in the next section.