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# Run SED-ML file
te.executeSEDML(sedmlStr)
# ### Execute Combine Archive
# Executing the SED-ML from a combine archive.
# In[2]:
import tellurium as te
from tellurium.tests.testdata import sedxDir
import os
omexPath = os.path.join(sedxDir, "BIOMD0000000003.sedx")
print(omexPath)
te.executeSEDML(omexPath)
# ### phrasedml experiment
# Tellurium provides support for simulation descriptions in SED-ML the export in Combine Archive format.
# In[3]:
import tellurium as te
antimony = '''
model myModel
S1 -> S2; k1*S1
S1 = 10; S2 = 0
k1 = 1
end
'''
# Applying postprocessing
plot "Figure 1.3 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 SED-ML
sedmlStr = phrasedml.convertString(phrasedmlStr)
if sedmlStr == None:
print(phrasedml.getLastError())
# Run the SED-ML file with results written in workingDir
import tempfile
import shutil
workingDir = tempfile.mkdtemp(suffix="_sedml")
te.executeSEDML(sedmlStr, workingDir=workingDir)
shutil.rmtree(workingDir)
# ### Execute Combine Archive
# Executing the SED-ML from a combine archive.
# In[2]:
import tellurium as te
from tellurium.tests.testdata import omexDir
import os
omexPath = os.path.join(omexDir, "BIOMD0000000003.sedx")
print(omexPath)
te.executeSEDML(omexPath)
# Applying preprocessing
plot "Figure 1.2 Timecourse after pre-processing" task2.time vs task2.PX, task2.PZ, task2.PY
# Applying postprocessing
plot "Figure 1.3 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 SED-ML
sedmlStr = phrasedml.convertString(phrasedmlStr)
if sedmlStr == None:
print(phrasedml.getLastError())
# Run SED-ML file
te.executeSEDML(sedmlStr)
# ### Execute Combine Archive
# Executing the SED-ML from a combine archive.
# In[2]:
import tellurium as te
from tellurium.tests.testdata import sedxDir
import os
omexPath = os.path.join(sedxDir, "BIOMD0000000003.sedx")
print(omexPath)
te.executeSEDML(omexPath)
# ### phrasedml experiment
def executeOmex(self):
""" Executes this Omex instance.
:return:
"""
import phrasedml
phrasedml.clearReferencedSBML()
workingDir = tempfile.mkdtemp(suffix="_sedml")
self.writeFiles(workingDir)
from tellurium import executeSEDML
for sedml_asset in self.getSedmlAssets():
if sedml_asset.getMaster():
sedml_path = os.path.join(workingDir, sedml_asset.getLocation())
executeSEDML(sedml_path,
workingDir=os.path.dirname(sedml_path))
# shutil.rmtree(workingDir)
workingDir = tempfile.mkdtemp(suffix="_sedml")
te.executeSEDML(sedmlStr, workingDir=workingDir)
shutil.rmtree(workingDir)
# ### Execute Combine Archive
# Executing the SED-ML from a combine archive.
# In[2]:
import tellurium as te
from tellurium.tests.testdata import omexDir
import os
omexPath = os.path.join(omexDir, "BIOMD0000000003.sedx")
print(omexPath)
te.executeSEDML(omexPath)
# ### phrasedml experiment
# Tellurium provides support for simulation descriptions in SED-ML the export in Combine Archive format.
# In[3]:
import tellurium as te
antimony = '''
model myModel
S1 -> S2; k1*S1
S1 = 10; S2 = 0
k1 = 1
end
'''