def get_sbml_biomodel(self, Biomodels_ID, **kwargs):
"""Get SBML model from biomodel.
Parameters: the ID for the Biomodels
Returns: the sbml in string format, export the SBML model into .xml file
"""
urn = "urn:miriam:biomodels.db:" + Biomodels_ID
sbml_str = temiriam.getSBMLFromBiomodelsURN(urn=urn)
# modify the format exported from Biomodel to the proper xml format
sbml_str = sbml_str.replace("><", "> <") # for the last line
sbml_str = sbml_str.replace("> ", ">\n ")
sbml_str = sbml_str.replace(" </sbml", "</sbml")
filepath = os.path.join(self.workingdir0, Biomodels_ID + ".xml")
for key, value in kwargs.items():
if "outputfile" in key:
filepath = value
with open(filepath, "wb") as f:
f.write(sbml_str.encode("utf-8"))
print("The SBML file path: ", filepath)
return sbml_str
def test_getSBMLFromBiomodelsURN1():
""" Check that string is returned.
:return:
"""
urn = 'urn:miriam:biomodels.db:BIOMD0000000139'
sbml = temiriam.getSBMLFromBiomodelsURN(urn)
assert sbml is not None
# check that string
assert isinstance(sbml, string_types)
def test_getSBMLFromBiomodelsURN1():
""" Check that model can be loaded in roadrunner.
:return:
"""
urn = 'urn:miriam:biomodels.db:BIOMD0000000139'
sbml = temiriam.getSBMLFromBiomodelsURN(urn)
print("*" * 80)
print(type(sbml))
print("*" * 80)
print(sbml)
print("*" * 80)
r = roadrunner.RoadRunner(sbml)
assert r is not None
from tellurium.sedml.mathml import *
import numpy as np
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d
import libsedml
import pandas
import os.path
workingDir = '/home/mkoenig/git/tellurium/tellurium/tests/testdata/sedml/sedx/_te_BIOMD0000000139'
# --------------------------------------------------------
# Models
# --------------------------------------------------------
# Model <model1>
import tellurium.temiriam as temiriam
__model1_sbml = temiriam.getSBMLFromBiomodelsURN('urn:miriam:biomodels.db:BIOMD0000000139')
model1 = te.loadSBMLModel(__model1_sbml)
# --------------------------------------------------------
# Tasks
# --------------------------------------------------------
# Task <task1>
# Task: <task1>
task1 = [None]
model1.setIntegrator('cvode')
model1.timeCourseSelections = ['Total_NFkBn', 'time']
task1[0] = model1.simulate(start=0.0, end=2500.0, steps=1000)
# --------------------------------------------------------
# DataGenerators
# --------------------------------------------------------
import numpy as np
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d
import libsedml
import pandas
import os.path
workingDir = '/home/mkoenig/git/tellurium/tellurium/tests/testdata/sedml/sed-ml'
# --------------------------------------------------------
# Models
# --------------------------------------------------------
# Model <model1>
import tellurium.temiriam as temiriam
__model1_sbml = temiriam.getSBMLFromBiomodelsURN(
'urn:miriam:biomodels.db:BIOMD0000000021')
model1 = te.loadSBMLModel(__model1_sbml)
# --------------------------------------------------------
# Tasks
# --------------------------------------------------------
# Task <task1>
# Task: <task1>
task1 = [None]
model1.setIntegrator('cvode')
model1.timeCourseSelections = [
'[P0]', '[T1]', '[T0]', '[CC]', '[P2]', '[T2]', '[P1]', '[Cn]', '[Mp]',
'time', '[Mt]'
]
task1[0] = model1.simulate(start=0.0, end=100.0, steps=1000)
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)
# <SBML species>
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
# <SBML parameters>
# 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
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)
# <SBML species>
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
# <SBML parameters>
# 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
def test_repressilator(self):
# 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)
assert return_code # valid SBML
# <SBML species>
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
# <SBML parameters>
# 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 = """
model1 = model "{}"
model2 = model model1 with ps_0=1.3E-5, ps_a=0.013
sim1 = simulate uniform(0, 1000, 1000)
task1 = run sim1 on model1
task2 = run sim1 on model2
# A simple timecourse simulation
plot "Timecourse of repressilator" task1.time vs task1.PX, task1.PZ, task1.PY
# Applying preprocessing
plot "Timecourse after pre-processing" task2.time vs task2.PX, task2.PZ, task2.PY
# Applying postprocessing
plot "Timecourse after post-processing" task1.PX/max(task1.PX) vs task1.PZ/max(task1.PZ), \
task1.PY/max(task1.PY) vs task1.PX/max(task1.PX), \
task1.PZ/max(task1.PZ) vs task1.PY/max(task1.PY)
""".format(urn)
# convert to sedml
print(phrasedml_str)
sedml_str = phrasedml.convertString(phrasedml_str)
if sedml_str is None:
print(phrasedml.getLastError())
raise IOError("sedml could not be generated")
# run SEDML directly
try:
tmp_dir = tempfile.mkdtemp()
executeSEDML(sedml_str, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)
# create combine archive and execute
try:
tmp_dir = tempfile.mkdtemp()
sedml_location = "repressilator_sedml.xml"
sedml_path = os.path.join(tmp_dir, sedml_location)
omex_path = os.path.join(tmp_dir, "repressilator.omex")
with open(sedml_path, "w") as f:
f.write(sedml_str)
entries = [
omex.Entry(location=sedml_location, formatKey="sedml", master=True)
]
omex.combineArchiveFromEntries(omexPath=omex_path, entries=entries, workingDir=tmp_dir)
executeCombineArchive(omex_path, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)
def test_repressilator(self):
# 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)
assert return_code # valid SBML
# <SBML species>
# PX - LacI protein
# PY - TetR protein
# PZ - cI protein
# X - LacI mRNA
# Y - TetR mRNA
# Z - cI mRNA
# <SBML parameters>
# 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 = """
model1 = model "{}"
model2 = model model1 with ps_0=1.3E-5, ps_a=0.013
sim1 = simulate uniform(0, 1000, 1000)
task1 = run sim1 on model1
task2 = run sim1 on model2
# A simple timecourse simulation
plot "Timecourse of repressilator" task1.time vs task1.PX, task1.PZ, task1.PY
# Applying preprocessing
plot "Timecourse after pre-processing" task2.time vs task2.PX, task2.PZ, task2.PY
# Applying postprocessing
plot "Timecourse after post-processing" task1.PX/max(task1.PX) vs task1.PZ/max(task1.PZ), \
task1.PY/max(task1.PY) vs task1.PX/max(task1.PX), \
task1.PZ/max(task1.PZ) vs task1.PY/max(task1.PY)
""".format(urn)
# convert to sedml
print(phrasedml_str)
sedml_str = phrasedml.convertString(phrasedml_str)
if sedml_str is None:
print(phrasedml.getLastError())
raise IOError("sedml could not be generated")
# run SEDML directly
try:
tmp_dir = tempfile.mkdtemp()
executeSEDML(sedml_str, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)
# create combine archive and execute
try:
tmp_dir = tempfile.mkdtemp()
sedml_location = "repressilator_sedml.xml"
sedml_path = os.path.join(tmp_dir, sedml_location)
omex_path = os.path.join(tmp_dir, "repressilator.omex")
with open(sedml_path, "w") as f:
f.write(sedml_str)
entries = [
omex.Entry(location=sedml_location,
formatKey="sedml",
master=True)
]
omex.combineArchiveFromEntries(omexPath=omex_path,
entries=entries,
workingDir=tmp_dir)
executeCombineArchive(omex_path, workingDir=tmp_dir)
finally:
shutil.rmtree(tmp_dir)