def create_distrib(tmp=False): """ Create demo model. :return: """ factory = Factory(modules=['sbmlutils.examples.models.distrib.distrib_ex1'], target_dir=os.path.join(models_dir, 'results')) factory.create(tmp)
def create(tmp=False): """ Create demo model. :return: """ models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__))) factory = Factory(modules=['sbmlutils.examples.models.example1.model'], target_dir=os.path.join(models_dir, 'results')) factory.create(tmp)
def create(tmp=False): """ Create model. :return: """ models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__))) print('-' * 80) print(models_dir) print('-' * 80) factory = Factory(modules=['sbmlutils.examples.models.assignment.model'], target_dir=os.path.join(models_dir, 'results')) factory.create(tmp)
def create(tmp=False): """ Create demo model. :return: """ models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__))) print('-'*80) print(models_dir) print('-' * 80) factory = Factory(modules=['sbmlutils.examples.models.tiny_model.model'], target_dir=os.path.join(models_dir, 'results'), annotations=os.path.join(models_dir, 'annotations.xlsx')) factory.create(tmp)
def create(tmp=False): """ Create demo model. :return: """ models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__))) print('-' * 80) print(models_dir) print('-' * 80) factory = Factory(modules=['sbmlutils.examples.models.demo.model'], target_dir=os.path.join(models_dir, 'results'), annotations=os.path.join(models_dir, 'demo_annotations.xlsx')) factory.create(tmp) # without annotations factory_no_annotations = Factory( modules=['sbmlutils.examples.models.demo.model'], target_dir=os.path.join(models_dir, 'results'), mid="{}_{}_{}".format(model.mid, model.version, "no_annotations")) factory_no_annotations.create(tmp)
def create(tmp: bool = False) -> None: factory = Factory( modules=["sbmlutils.examples.models.initial_assignment.model"], output_dir=Path(__file__).parent / "results", ) factory.create(tmp)
# --------------------------------------------------------------------------------------------------------------------- # Assignments # --------------------------------------------------------------------------------------------------------------------- assignments = [ InitialAssignment("S1", "10.0 mM", UNIT_mM), ] # --------------------------------------------------------------------------------------------------------------------- # Rules # --------------------------------------------------------------------------------------------------------------------- rules = [] # --------------------------------------------------------------------------------------------------------------------- # Reactions # --------------------------------------------------------------------------------------------------------------------- reactions = [] if __name__ == "__main__": import os from sbmlutils.modelcreator.creator import Factory models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__))) factory = Factory( modules=["sbmlutils.examples.models.example1.model"], output_dir=os.path.join(models_dir, "results"), ) factory.create()
# # The list of tuples can be provided on object generation # # ``` # Species(sid='e__gal', compartment='ext', initialConcentration=3.0, # substanceUnit=UNIT_KIND_MOLE, boundaryCondition=True, # name='D-galactose', sboTerm=SBO_SIMPLE_CHEMICAL, # annotations=[ # (BQB.IS, "bigg.metabolite/gal"), # galactose # (BQB.IS, "chebi/CHEBI:28061"), # alpha-D-galactose # (BQB.IS, "vmhmetabolite/gal"), # ] # ), # ``` # # For the full example see [model_with_annotations.py](./model_with_annotations.py) # In[4]: import os from sbmlutils.modelcreator.creator import Factory factory = Factory(modules=['model_with_annotations'], target_dir='./models') [_, _, sbml_path] = factory.create() # check the annotations on the species import libsbml doc = libsbml.readSBMLFromFile(sbml_path) # type: libsbml.SBMLDocument model = doc.getModel() # type: libsbml.Model s1 = model.getSpecies('e__gal') # type: libsbml.Species print(s1.toSBML())
]) # --------------------------------------------------------------------------------------------------------------------- # Assignments # --------------------------------------------------------------------------------------------------------------------- assignments = [ InitialAssignment('S1', '10.0 mM', UNIT_mM), ] # --------------------------------------------------------------------------------------------------------------------- # Rules # --------------------------------------------------------------------------------------------------------------------- rules = [] # --------------------------------------------------------------------------------------------------------------------- # Reactions # --------------------------------------------------------------------------------------------------------------------- reactions = [ ] if __name__ == "__main__": import os from sbmlutils.modelcreator.creator import Factory models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__))) factory = Factory(modules=['sbmlutils.examples.models.example1.model'], target_dir=os.path.join(models_dir, 'results')) factory.create()
import cobra from cobra.io import read_sbml_model # ----------------------------------------------------------------------------- # create model # ----------------------------------------------------------------------------- models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__))) print('-'*80) print(models_dir) print('-' * 80) factory = Factory(modules=['sbmlutils.examples.models.tiny_model.model'], target_dir=os.path.join(models_dir, 'results'), annotations=os.path.join(models_dir, 'annotations.xlsx')) _, _, tiny_sbml = factory.create(tmp=False) # ----------------------------------------------------------------------------- # run ode simulation # ----------------------------------------------------------------------------- # tiny_sbml = os.path.join(os.path.dirname(os.path.abspath(__file__)), # 'results', # '{}_{}.xml'.format(model.mid, model.version)) r = roadrunner.RoadRunner(tiny_sbml) r.timeCourseSelections = ["time"] + r.model.getBoundarySpeciesIds() + r.model.getFloatingSpeciesIds() + r.model.getReactionIds() + r.model.getGlobalParameterIds() r.timeCourseSelections += ["[{}]".format(key) for key in r.model.getFloatingSpeciesIds()] # print(r) s = r.simulate(0, 400, steps=400)
def create(tmp: bool = False) -> None: factory = Factory( modules=["sbmlutils.examples.models.boundary_condition_2.model"], output_dir=Path(__file__).parent / "results", ) factory.create(tmp)
import cobra from cobra.io import read_sbml_model # ----------------------------------------------------------------------------- # create model # ----------------------------------------------------------------------------- models_dir = os.path.join(os.path.dirname(os.path.abspath(__file__))) print('-' * 80) print(models_dir) print('-' * 80) factory = Factory(modules=['sbmlutils.examples.models.tiny_model.model'], target_dir=os.path.join(models_dir, 'results'), annotations=os.path.join(models_dir, 'annotations.xlsx')) _, _, tiny_sbml = factory.create(tmp=False) # ----------------------------------------------------------------------------- # run ode simulation # ----------------------------------------------------------------------------- # tiny_sbml = os.path.join(os.path.dirname(os.path.abspath(__file__)), # 'results', # '{}_{}.xml'.format(model.mid, model.version)) r = roadrunner.RoadRunner(tiny_sbml) r.timeCourseSelections = [ "time" ] + r.model.getBoundarySpeciesIds() + r.model.getFloatingSpeciesIds( ) + r.model.getReactionIds() + r.model.getGlobalParameterIds() r.timeCourseSelections += [ "[{}]".format(key) for key in r.model.getFloatingSpeciesIds()