Our models are generally developed and analysed using ScrumPy, and the ScrumPy source files are human--readable text files (*.spy). (Unless otherwise stated, these files will have Linux/MacOS line ends, and Windows users should either convert the line ends or open them with a text editor that copes with the difference.) SBML forms are provided for compatibility.
These model files contain the metabolic network structure only. Constraints (including biomass composition) and objectives for analysis by linear programming / FBA are in associated Python modules to be used in conjunction with ScrumPy. Contact us for further details.