Downloads - SimPheny to SBML

Generates SBML file WITH simulation specific data Level 2 version 1 (simpheyny_to_sbml_l2v1_flux.pl)

SBML file will contain reconstruction

• reactions (format: ‘R_<reaction abbreviation >’)

   

  • reaction name, reversibility, reaction stoichiometry, gene-protein-reaction (GPR) association, subsystem, E.C. number
• metabolites (format: ‘M_<metabolite abbreviation>_<compartment abbreviation>’)

   

  • metabolite name, compartment, charge, formula (appended to the end of the name, <metabolite name>_FORMULA)

     

• a flux distribution associated with a steady-state modeling simulation
  • lower bound, upper bound, objective coefficient, flux value, reduced cost

Generates SBML file WITHOUT simulation specific data Level 2 version 1 (simpheny_to_sbml_l2v1.pl)

SBML file will contain reconstruction

• reactions (format: ‘R_<reaction abbreviation >’)
  • reaction name, reversibility, reaction stoichiometry, gene-protein-reaction (GPR) association, subsystem, E.C. number
• metabolites (format: ‘M_<metabolite abbreviation>_<compartment abbreviation>’)
  • metabolite name, compartment, charge, formula (appended to the end of the name, <metabolite name>_FORMULA)

Changes to the SBML generating code: change log