Design principles

  • Proteins should be separated from metabolites and reactions at the user-level

model.metabolites
model.reactions
model.proteins

  • Writable models that comply with community standard (SBML) without hacks.

  • Experimental data should be easy to load.

SBML compliance

Proteins are Species:

  • in Group (SBML extension) Proteins;

  • with initialAmount (optional): concentration (double);

  • and kcat value (double) in reaction stoichiometry.

Protein Exchanges:

  • Not present in the SBML file.

  • Generated at the time of parsing.

For backwards compatibility, with the available enzyme constrained models, read_sbml_ec_model also parses ungroupped metabolites with following the naming convention prot_{UNIPROT_ID}.

...
<listOfSpecies>
    <species id="prot_P00363" compartment="c" initialAmount="0.12"/>
    <species id="prot_P08921" compartment="c" initialAmount="1.4"/>
</listOfSpecies>
<listOfGroups xmlns="http://www.sbml.org/sbml/level3/version1/groups/version1">
    <group kind="classification" id="Protein">
        <listOfMembers id="all_proteins">
            <member idRef="prot_P00363"/>
            <member idRef="prot_P08921"/>
        </listOfMembers>
    </group>
</listOfGroups>
...