B subtilis SBML

B. subtilis SBML files

SBML files contain reconstruction (see sbml.org for documentation)

reactions (format: ‘R_’)

reaction name, reversibility, reaction stoichiometry, gene-protein-reaction (GPR) association, subsystem, E.C. number

metabolites (format: ‘M__’)

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

a flux distribution associated with a steady-state modeling simulation

lower bound, upper bound, objective coefficient, flux value, reduced cost


iYO844 Published in J. Biol. Chem. (2007)

(1020 Reactions)

SBML (level 2, version 1) w/ a flux distribution: Bs_iYO844_flux1.xml

File info for iYO844:

SBML File Properties
file name Bs\_iYO844\_flux1.xml
organism Bacillus subtilis
model iYO844
Biomass Objective Function (BOF) BS\_Biomass\_10
flux balance analysis objective maximize BOF
Growth Associated Maintenance (GAM) 105 mmol ATP gDW–1
Non-Growth Associated Maintenance (NGAM) 9 mmol ATP gDW–1 hr–1
media conditions computational minimal media (see publication)
carbon source 1.7 mmol glucose gDw–1 hr–1
aerobic or anaerobic 1000 mmol O2 gDw–1 hr–1 (unconstrained, aerobic)
additional constraints
reactions constrained to zero none (CYOO3 was not restricted in this simulation)
flux split between reaction pairs none

SBML files are periodically updated. For changes, see the Change Log.



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