Simpheny Perl Application

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

Location

Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

Contact Us

Contact Us

In Silico Lab:  858-822-1144

Wet Lab:  858-246-1625

FAX:   858-822-3120

Website Concerns: sbrgit@ucsd.edu

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