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
Reconstructions
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.