SBMLfill example: phosphofructokinase reaction

Back to SBMLfill online.

PFK reaction As an example, we have implemented the phosphofructokinase reaction (KEGG reaction R04779) in the SBML model pfk_reaction.xml. The tab-separated data file pfk_parameter_values.tsv contains a table with all model parameters (arbitrary values)

Table columns SBMLfill recognises columns by their headers. The mandatory columns are "QuantityType", "Value", "Compound", and "Reaction". The columns "Compound" and "Reaction" refer to the reaction ids and species ids used in the SBML file. The columns "Quantity", "Unit","CompoundName", "EnzymeName", "CompoundID:obo.chebi", and "EnzymeID:ec-code" are not used by SBMLfill. They have only been inserted to relate the quantities to the diagram shown above. Unknown columns will be ignored. A table with the minimal required rows would look like this:

Model parameters Missing parameters will be replaced by default values of 1. Parameters not matching the model are ignored. If parameters appear several times, only the last value is used. Enzymes are described by concentrations unless enzyme amounts are given in the parameter table.

Example output The resulting model for the default choices (Reversible Power law, Catalytic rate constants, Essential activiation, Non-competetive inhibition) should look like this: pfk_reaction_filled_PM.xml