PSAMM: A Portable System for the Analysis of Metabolic Models
Fig 3
An illustration of the PSAMM YAML format.
(a) This diagram shows an example of the YAML model format, which includes a central model definition (model.yaml) and multiple annotation files. Each box indicates a file with a possible filename indicated above the box, and the text within is a snapshot of the file content. (b) An example showing how changes can be tracked in a PSAMM YAML file (biomass.yaml) using the Git version control system in command line. The text highlighted in red indicates the stoichiometry of the compound arg-L in an old version of the biomass function, while the text highlighted in green indicates the updated value in a new version of the model. Additional examples of applying Git version control on the YAML format are provided in the supplemental materials (S2–S5 Texts).