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# ### SED-ML L1V2 specification example
# Repressilator example which demonstrates the use of phrasedml with URN examples.
#
# The examples are the reference examples from the SED-ML specification document available from http://sed-ml.sourceforge.net/documents/sed-ml-L1V2.pdf (Introduction Section).
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
import phrasedml
# Get SBML from URN and set for phrasedml
urn = "urn:miriam:biomodels.db:BIOMD0000000012"
sbmlStr = te.temiriam.getSBMLFromBiomodelsURN(urn=urn)
phrasedml.setReferencedSBML(urn, sbmlStr)
#
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
#
# ps_a - tps_active: Transcrition from free promotor in transcripts per second and promotor
# ps_0 - tps_repr: Transcrition from fully repressed promotor in transcripts per second and promotor
phrasedmlStr = """
model1 = model "{}"
# ### SED-ML L1V2 specification example
# Repressilator example which demonstrates the use of phrasedml with URN examples.
#
# The examples are the reference examples from the SED-ML specification document available from http://sed-ml.sourceforge.net/documents/sed-ml-L1V2.pdf (Introduction Section).
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
import phrasedml
# Get SBML from URN and set for phrasedml
urn = "urn:miriam:biomodels.db:BIOMD0000000012"
sbmlStr = te.temiriam.getSBMLFromBiomodelsURN(urn=urn)
phrasedml.setReferencedSBML(urn, sbmlStr)
#
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
#
# ps_a - tps_active: Transcrition from free promotor in transcripts per second and promotor
# ps_0 - tps_repr: Transcrition from fully repressed promotor in transcripts per second and promotor
phrasedmlStr = """
model1 = model "{}"
Model is repressilator.
"""
from __future__ import absolute_import, print_function
import os
import tempfile
import shutil
from tellurium import temiriam
from tellurium.sedml.tesedml import executeCombineArchive, executeSEDML
from tellurium.utils import omex
import phrasedml
# Get SBML from URN and set for phrasedml
urn = "urn:miriam:biomodels.db:BIOMD0000000012"
sbml_str = temiriam.getSBMLFromBiomodelsURN(urn=urn)
return_code = phrasedml.setReferencedSBML(urn, sbml_str)
print('valid SBML', return_code)
#
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
#
# ps_a - tps_active: Transcription from free promotor in transcripts per second and promotor
# ps_0 - tps_repr: Transcription from fully repressed promotor in transcripts per second and promotor
phrasedml_str = """
import roadrunner
from tellurium.temiriam import getSBMLFromBiomodelsURN
print("Get SBML from URN")
# urn = 'urn:miriam:biomodels.db:BIOMD0000000003'
urn = 'urn:miriam:biomodels.db:BIOMD0000000139'
sbml = getSBMLFromBiomodelsURN(urn)
print(sbml)
print(type(sbml))
import roadrunner
r = roadrunner.RoadRunner(sbml)
print(r)