def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = '"End of code generated by Import Combine as PhrasedML plugin ' + time.strftime(
"%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(os.path.join(zipextloc, sbmlloclist[i]))
try:
transtext = te.sbmlToAntimony(sbml)
except Exception as e:
transtext = """*********************WARNING*********************
Failed to translate the SBML model to Antimony string.
Please check that the SBML file is valid.
*********************WARNING*********************"""
transtext = transtext + "\n\n" + str(e)
sbmlstrlist.append(transtext)
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(os.path.join(zipextloc, sedmlloclist[j]))
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(
"AntimonyModel = '''\n" + sbmlstrlist[0] +
"'''\n\nPhrasedMLstr = '''\n" + sedmlstrlist[k] +
"'''\n\nimport tellurium as te\n\nexp = te.experiment([AntimonyModel], [PhrasedMLstr])\nexp.execute(PhrasedMLstr)\n\n"
+ outputstr)
delseq(zipextloc)
return outputstrlist
def getSBMLAsAntimony(self, sbmlfile):
zf = ZipFile(self.combinePath, 'r')
sbmlStr = zf.read(sbmlfile)
zf.close()
antStr = te.sbmlToAntimony(sbmlStr)
return antStr
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = "# -*- coding: utf-8 -*-\n\n" + '"Generated by Import Combine with PhrasedML plugin ' + time.strftime(
"%m/%d/%Y"
) + '"\n"Extracted from ' + filename + '"\n\n# Translated SBML\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(zipextloc + sedmlloclist[j])
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(outputstr + "AntimonyModel = '''\n" +
sbmlstrlist[0] +
"'''\n\nPhrasedMLstr = '''\n" +
sedmlstrlist[k] + "'''")
delseq(zipextloc)
return outputstrlist
def selected_part(self):
from tellurium.visualization import SBMLDiagram
from tellurium.analysis import _annotations, make_submodel
import tellurium as te
self.set_visible(5)
r = self.widgets['reactionResults'].value
biomodel_id = _annotations.get_biomodel_id(r.model.getSBMLDocument())
self.sbml = self.matched_sbml_lookup[biomodel_id]
self.submodel = make_submodel(r)
antimony = te.sbmlToAntimony(self.submodel.toSBML())
self.widgets['selectedReaction'].children[1].value = antimony
# Draw diagram
diagram = SBMLDiagram(self.submodel, reactions={
'shape': 'box'
})
img = diagram.draw(layout='dot')
self.widgets['selectedReaction'].children[0].value = img.data
# Modular import code snippet
self.widgets['selectedReaction'].children[2].value = '''!pip install git+https://github.com/biomodels/%s.git > /dev/null
# Modular Import of Biomodel reaction
import %s as m
import tellurium as te
from tellurium.analysis import make_submodel
r = m.sbml.model.getReaction('%s')
submodel = make_submodel(r)
antimony = te.sbmlToAntimony(submodel.toSBML())
print antimony
''' % (biomodel_id, biomodel_id, r.getId())
def load_and_translate(self, sbmlfile, pythonfile, editor, set_current=True):
"""
Read filename as combine archive, unzip, translate, reconstitute in
Python, and create an editor instance and return it
*Warning* This is loading file, creating editor but not executing
the source code analysis -- the analysis must be done by the editor
plugin (in case multiple editorstack instances are handled)
"""
sbmlfile = str(sbmlfile)
self.emit(SIGNAL('starting_long_process(QString)'),
_("Loading %s...") % sbmlfile)
text, enc = encoding.read(sbmlfile)
sbmlstr = te.readFromFile(sbmlfile)
text = "import tellurium as te\n\nr = te.loada('''\n" + str(te.sbmlToAntimony(sbmlstr)) + "''')"
widgeteditor = editor.editorstacks[0]
finfo = widgeteditor.create_new_editor(pythonfile, enc, text, set_current, new=True)
index = widgeteditor.data.index(finfo)
widgeteditor._refresh_outlineexplorer(index, update=True)
self.emit(SIGNAL('ending_long_process(QString)'), "")
if widgeteditor.isVisible() and widgeteditor.checkeolchars_enabled \
and sourcecode.has_mixed_eol_chars(text):
name = os.path.basename(pythonfile)
QMessageBox.warning(self, widgeteditor.title,
_("<b>%s</b> contains mixed end-of-line "
"characters.<br>Spyder will fix this "
"automatically.") % name,
QMessageBox.Ok)
widgeteditor.set_os_eol_chars(index)
widgeteditor.is_analysis_done = False
finfo.editor.set_cursor_position('eof')
finfo.editor.insert_text(os.linesep)
return finfo, sbmlfile
def getComponentAntimony(self):
'''
Returns list of antimony models generated from each model reaction
'''
import tellurium as te
sbmls = self.getComponentSBML()
return [te.sbmlToAntimony(sbml) for sbml in sbmls]
def configpossiblechecker(sbmlstr):
antimony_str = te.sbmlToAntimony(sbmlstr)
is_match = bool(re.search('function', antimony_str))
if is_match == True:
raise NotImplementedError(
'SBML string is too complex for module to convert')
else:
return
def sbmltoantimony(sbmlfile):
"""Get the sbml file and return the antimony string."""
antimony_str = te.sbmlToAntimony(sbmlfile)
basename = os.path.basename(sbmlfile)
sbmlfilename = basename.split(".")[0]
antimony_str = antimony_str.replace("doc0", sbmlfilename)
return antimony_str
def getSBMLAsAntimony(self, sbmlfile):
""" returns SBML as antimony
:param sbmlfile: filename of SBML file in COMBINE archive
:return: antimony string
:rtype: str
"""
zf = ZipFile(self.combinePath, 'r')
sbmlStr = zf.read(sbmlfile)
zf.close()
antStr = te.sbmlToAntimony(sbmlStr)
return antStr
def getSBMLAsAntimony(self, sbmlfile):
""" returns SBML as antimony
:param sbmlfile: filename of SBML file in COMBINE archive
:return: antimony string
:rtype: str
"""
warnings.warn('Use inline_omex instead.', DeprecationWarning)
zf = ZipFile(self.combinePath, 'r')
sbmlStr = zf.read(sbmlfile)
zf.close()
antStr = te.sbmlToAntimony(sbmlStr)
return antStr
def getSBMLAsAntimony(self, sbmlfile):
""" returns SBML as antimony
:param sbmlfile: filename of SBML file in COMBINE archive
:return: antimony string
:rtype: str
"""
warnings.warn('Use inline_omex instead.', DeprecationWarning)
zf = ZipFile(self.combinePath, 'r')
sbmlStr = zf.read(sbmlfile)
zf.close()
antStr = te.sbmlToAntimony(sbmlStr)
return antStr
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
rePath = r"loadSBMLModel\((.*)\)"
reFig = r"savefig\((.*)\)"
outputstr = '"End of code generated by Import Combine plugin ' + time.strftime(
"%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(os.path.join(zipextloc, sbmlloclist[i]))
try:
transtext = te.sbmlToAntimony(sbml)
except Exception as e:
transtext = """*********************WARNING*********************
Failed to translate the SBML model to Antimony string.
Please check that the SBML file is valid.
*********************WARNING*********************"""
transtext = transtext + "\n\n" + str(e)
sbmlstrlist.append(transtext)
for j in range(len(sedmlloclist)):
sedmlstr = te.sedmlToPython(
os.path.join(zipextloc, sedmlloclist[j]))
lines = sedmlstr.splitlines()
for i, s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
s = s.replace("loadSBMLModel", "loada")
s = s.replace(reSearchPath[1], "AntimonyModel")
lines[i] = s
lines.insert(
i - 1,
"AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n")
for i, s in enumerate(lines):
reSearchFig = re.split(reFig, s)
if len(reSearchFig) > 1:
del lines[i]
sedmlstr = '\n'.join(lines)
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(sedmlstrlist[k] + '\n\n' + outputstr)
delseq(zipextloc)
return outputstrlist
def generateNetworkFromSBML(sbml):
"""
Generate network matrix from a given model
:param sbml: sbml string or file path
:rtype: array
"""
import roadrunner
import tellurium as te
try:
ant_str = te.sbmlToAntimony(sbml)
except:
raise Exception("Cannot load SBML file/string. Check whether the \
filepath or SBML string is formatted correctly.")
net_mat, ref_list = generateNetworkFromAntimony(ant_str)
return net_mat, ref_list
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = "# -*- coding: utf-8 -*-\n\n" + '"Generated by Import Combine with PhrasedML plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n\n# Translated SBML\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(zipextloc + sedmlloclist[j])
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(outputstr + "AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n\nPhrasedMLstr = '''\n" + sedmlstrlist[k] + "'''")
delseq(zipextloc)
return outputstrlist
def gen_dictionary(data):
'''
Passes XML data through beautifulsoup parser
making data more easily readable
:param data: SBML string in XML string format
:returns: all required data in list format
'''
antimony_str = te.sbmlToAntimony(data)
Bs_data = BeautifulSoup(data, "xml")
b_species = Bs_data.find_all('listOfSpecies')
species_store = Convert(str(b_species))
b_parameters = Bs_data.find_all('listOfParameters')
parameters_store = Convert(str(b_parameters))
b_reactions = Bs_data.find_all('listOfReactions')
reactions_store = Convert(str(b_reactions))
b_rules = Bs_data.find_all('listOfRules')
rules_store = Convert(str(b_rules))
#soup.find_all("a", class_="sister")
#print(Bs_data.find_all('div', class_='dc:description'))
if Bs_data.find_all(class_='dc:description') != []:
b_description = Bs_data.find_all(class_='dc:description')
description_store = Convert(str(b_description))
description_store = gen_description(description_store)
else:
description_store = ''
if Bs_data.find_all(class_='dc:bibliographicCitation') != []:
reference_store = gen_reference(Bs_data)
else:
reference_store = ''
'''
print(species_store, '\n')
print(parameters_store, '\n')
print(reactions_store, '\n')
print(rules_store, '\n')
'''
#print(description_store)
return species_store, parameters_store, reactions_store, rules_store, antimony_str, description_store, reference_store
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = '"End of code generated by Import Combine as PhrasedML plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(zipextloc + sedmlloclist[j])
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append("AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n\nPhrasedMLstr = '''\n" + sedmlstrlist[k] +
"'''\n\nimport tellurium as te\n\nexp = te.experiment([AntimonyModel], [PhrasedMLstr])\nexp.execute(PhrasedMLstr)\n\n" + outputstr)
delseq(zipextloc)
return outputstrlist
def spark_sensitivity_analysis(model_with_parameters):
import tellurium as te
sa_model = model_with_parameters[0]
parameters = model_with_parameters[1]
class_name = importlib.import_module(sa_model.filename)
user_defined_simulator = getattr(class_name, dir(class_name)[0])
sa_model.simulation = user_defined_simulator()
if (sa_model.sbml):
model_roadrunner = te.loadAntimonyModel(
te.sbmlToAntimony(sa_model.model))
else:
model_roadrunner = te.loadAntimonyModel(sa_model.model)
model_roadrunner.conservedMoietyAnalysis = sa_model.conservedMoietyAnalysis
#Running PreSimulation
model_roadrunner = sa_model.simulation.presimulator(model_roadrunner)
#Running Analysis
computations = {}
model_roadrunner = sa_model.simulation.simulator(
model_roadrunner, computations)
_analysis = [None, None]
#Setting the Parameter Variables
_analysis[0] = {}
for i_param, param_names in enumerate(sa_model.bounds.keys()):
_analysis[0][param_names] = parameters[i_param]
setattr(model_roadrunner, param_names, parameters[i_param])
_analysis[1] = computations
return _analysis
def spark_sensitivity_analysis(model_with_parameters):
import tellurium as te
sa_model = model_with_parameters[0]
parameters = model_with_parameters[1]
class_name = importlib.import_module(sa_model.filename)
user_defined_simulator = getattr(class_name, dir(class_name)[0])
sa_model.simulation = user_defined_simulator()
if(sa_model.sbml):
model_roadrunner = te.loadAntimonyModel(te.sbmlToAntimony(sa_model.model))
else:
model_roadrunner = te.loadAntimonyModel(sa_model.model)
model_roadrunner.conservedMoietyAnalysis = sa_model.conservedMoietyAnalysis
#Running PreSimulation
model_roadrunner = sa_model.simulation.presimulator(model_roadrunner)
#Running Analysis
computations = {}
model_roadrunner = sa_model.simulation.simulator(model_roadrunner,computations)
_analysis = [None,None]
#Setting the Parameter Variables
_analysis[0] = {}
for i_param,param_names in enumerate(sa_model.bounds.keys()):
_analysis[0][param_names] = parameters[i_param]
setattr(model_roadrunner, param_names, parameters[i_param])
_analysis[1] = computations
return _analysis
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
rePath = r"loadSBMLModel\((.*)\)"
reFig = r"savefig\((.*)\)"
outputstr = '"End of code generated by Import Combine plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = te.sedmlToPython(zipextloc + sedmlloclist[j])
lines = sedmlstr.splitlines()
for i,s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
s = s.replace("loadSBMLModel", "loada")
s = s.replace(reSearchPath[1],"AntimonyModel")
lines[i] = s
lines.insert(i - 1, "AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n")
for i,s in enumerate(lines):
reSearchFig = re.split(reFig, s)
if len(reSearchFig) > 1:
del lines[i]
sedmlstr = '\n'.join(lines)
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(sedmlstrlist[k] + '\n\n' + outputstr)
delseq(zipextloc)
return outputstrlist
# coding: utf-8
# Back to the main [Index](../index.ipynb)
# ### Test models
# 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
# To get the builtin models use listTestModels
print(te.listTestModels())
# #### Load test model
# In[2]:
# To load one of the test models use loadTestModel:
# r = te.loadTestModel('feedback.xml')
# result = r.simulate (0, 10, 100)
# r.plot (result)
# If you need to obtain the SBML for the test model, use getTestModel
sbml = te.getTestModel('feedback.xml')
# To look at one of the test model in Antimony form:
ant = te.sbmlToAntimony(te.getTestModel('feedback.xml'))
print(ant)
def test_sbmlToAntimony_str(self):
ant = te.sbmlToAntimony(self.sbml_str)
self.assertIsNotNone(ant)
def test_sbmlToAntimony_file(self):
ant = te.sbmlToAntimony(self.sbml_file)
self.assertIsNotNone(ant)
def test_sbmlToAntimony_file(self):
ant = te.sbmlToAntimony(self.sbml_file)
self.assertIsNotNone(ant)
import os, glob
import tellurium as te
from web_interface import SBML_FILE
model_string = ''
if model_string == '':
with open(SBML_FILE, 'r') as f:
sbml = f.read()
model_string = te.sbmlToAntimony(sbml)
if __name__ == '__main__':
print(model_string)
def test_sbmlToAntimony_str(self):
ant = te.sbmlToAntimony(self.sbml_str)
self.assertIsNotNone(ant)
def Combinecreator(core_model, settings, Plot_Variable, outputpath, KISAO_algorithm):
'''
Generates and outputs COMBINE OMEX file.
:param core_model: core model database of model
:param settings: settings database of model
:param Plot_Variable: Variables to be plotted in list format
:param outputpath: filepath to output OMEX file in OS path format
:param KISAO_algorithm: Kinetic Simulation Algorithm Ontology number in string format
:return combine_filename : OMEX file name in string format
:return total_scenarios : Total number of scenarios in string format
'''
#--- Extract data from settings and clean up units ---
number_init = len(settings['init'])
number_parameters = len(settings['parameters'])
addparam = settings['parameters']
unit_model = sbmlgen.unitlookup(settings)
total_scenarios = number_init * number_parameters
#print(total_scenarios)
scenario_name = core_model["system_type"]
scenario_name = scenario_name.replace(", ", "_")
modelname_file = []
antimony_final = []
#--- Generates SBML string and adds to list
#based on the number of combinations with init
#and parameter amts ---
for j in range(number_init): #Cycle through number of init
for k in range(number_parameters): #Cycle through number of parameters
sbmlstr = sbmlgen.SBMLcreation(core_model, settings, unit_model, addparam, j, k)
antimony_final.append(te.sbmlToAntimony(sbmlstr))
#--- Generates the scenario name for each SBML string generated ---
scenario_placeholder = []
for l in range(total_scenarios):
for j in range(number_init): #Cycle through number of init
for k in range(number_parameters):
temp_scenario_name = '_' + str(j+1)+ '_' + str(k+1)
scenario_placeholder.append(temp_scenario_name)
#--- Names the models in antimony string according the scenario ---
inline_omex = '\n'
for l in range(total_scenarios):
scenario_name = scenario_name + scenario_placeholder[l]
modelname_file.append(scenario_name)
antimony_final[l] = antimony_final[l].replace('*doc0', modelname_file[l])
scenario_name = scenario_name.replace(scenario_placeholder[l], "")
inline_omex = inline_omex + str(antimony_final[l])
#print("This is antimony_final", scenario_number,": \n", antimony_final[l])
#--- Generates phrasedml file ---
phrasedml_final = gen_phrasedml(settings, modelname_file, Plot_Variable, KISAO_algorithm)
#--- Generates and outputs OMEX file---
inline_omex = inline_omex + phrasedml_final
combine_filename = 'COMBINE_' + scenario_name + '.omex'
archive = os.path.join(outputpath, combine_filename)
print('COMBINE Archive output: ', archive)
te.exportInlineOmex(inline_omex, archive)
return combine_filename, total_scenarios
continue
if case == '00999':
continue
if int(case) > int(1085):
continue
try:
num_cases += 1
sbmlfname, sedmlfname = combine2python.manifestsearch(folder_path)
# sbml = [file for file in sorted(ls) if 'sbml-l2v4.xml' in file][0]
with open(path.join(folder_path, '.' + sbmlfname), 'rb') as f:
sbml = f.read()
rr = te.loada(te.sbmlToAntimony(sbml))
rr.simulate()
combine2python.codestitch('test' + str(case) + '.py', folder_path, case)
combine2python.codeanalysis('test' + str(case) + '.py', folder_path)
pyscriptname = 'test' + str(case)
test = __import__(pyscriptname)
num_timepoints = len(test.allX_0)
results_file = [file for file in ls if 'results.csv' in file][0]
computed_result = np.hstack([test.allX_0[:,0].reshape(num_timepoints, 1), test.allY_0])
with open(os.path.join(folder_path, results_file), 'rb') as f:
reader = csv.reader(f)
rows = []
for i, row in enumerate(reader):
if i == 0:
def translate(combine, filename):
tempPath = [[]]
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
rePath = r"(\w*).load\('(.*)'\)"
reLoad = r"(\w*) = roadrunner.RoadRunner\(\)"
reSelections = r'(\w+)\.selections = \[(.*),?\]'
outputstr = "# -*- coding: utf-8 -*-\n\n" + '"Generated by Import Combine plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n\n# Translated SBML\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = se.sedml_to_python(zipextloc + sedmlloclist[j])
lines = sedmlstr.splitlines()
for i,s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
modpath = getbasename(reSearchPath[2])[:-4].replace('-','_')
if modpath[0].isdigit() == True:
modpath = 'Model_' + modpath
tempPath.append([reSearchPath[1], modpath])
else:
tempPath.append([reSearchPath[1], modpath])
#if '.xml' in s:
del lines[i]
for i,s in enumerate(lines):
reSearchLoad = re.split(reLoad, s)
if len(reSearchLoad) > 1:
for k in range(len(tempPath) - 1):
if reSearchLoad[1] == tempPath[k + 1][0]:
s = s.replace("roadrunner.RoadRunner()", "te.loada(" + str(tempPath[k + 1][1])+ ")")
lines[i] = s
#if '"compartment"' or "'compartment'" in sedmlstr:
# reSearchSelections = re.split(reSelections, s)
# if len(reSearchSelections) > 1:
# Vars = reSearchSelections[2].replace(' ','').split(',')
# Vars = [s.replace('"','') for s in Vars]
# for i in range(len(Vars)):
# if Vars[i] == "compartment":
# Vars[i] = "compartment_"
if not "import tellurium" in sedmlstr:
if "import roadrunner" in sedmlstr:
for i,s in enumerate(lines):
if "import roadrunner" in s:
del lines[i]
lines.insert(i, "import tellurium as te")
else:
pass
else:
outputstr = outputstr + "import tellurium as te\n\n"
sedmlstr = '\n'.join(lines)
# List of replacements
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(outputstr + tempPath[1][1] + " = '''\n" + sbmlstrlist[0] + "'''\n\n" + sedmlstrlist[k])
delseq(zipextloc)
return outputstrlist
import BMSS.simulation as sim
if __name__ == '__main__':
'''
Use following function to create SBML from BIOModel online database
Outputs both the sbmlstring and the XML file
'''
Biomodels_ID = 'BIOMD0000000012'
#Input biomodels ID number
SBMLfilename = 'Repressilator_TestModel_SBML.xml' #Name the XML file
outputpath = str(Path.cwd()/SBMLfilename)
onlinemodelstr = onlinegen.get_online_biomodel(Biomodels_ID, outputfile=outputpath)
antimony_str = te.sbmlToAntimony(onlinemodelstr)
'''
Use the following function to create SBML from local folder.
XML file must be in same folder as this Tutorial
'''
inputpath = str(Path.cwd()/'Repressilator_TestModel_SBML_1.xml')
with open(inputpath, 'r', encoding='utf8', errors='ignore') as f:
localmodelstr = f.read()
'''
To create config ini file from SBML file in folder
Reading the data inside the xml file to a variable
import tellurium as te
# convert to eliminate rate rules
model = te.loadAntimonyModel(te.sbmlToAntimony('huang-ferrell-96.xml'))
model.conservedMoietyAnalysis = True
print(model.steadyStateNamedArray())
# need to pre-simulate to converge in COPASI's solution
model.simulate(0,1000,5000)
# the output variable is PP_K (which represents doubly phosphorylated MAPK)
# parameter 2: r1b_k2 (original: MAPKKK activation.k1)
fig1a_local = model.getCC('PP_K', 'r1b_k2')
print('Figure 1A: local value = {}'.format(fig1a_local))
# parameter 5: r8a_a8 (original: binding MAPK—Pase and P-MAPK.k1)
fig1b_local = model.getCC('PP_K', 'r8a_a8')
print('Figure 1B: local value = {}'.format(fig1b_local))
# parameter 7: r10a_a10 (original: binding MAPK—Pase and PP—MAPK.k1)
fig1c_local = model.getCC('PP_K', 'r10a_a10')
print('Figure 1C: local value = {}'.format(fig1c_local))
def sbmlconv(zipextloc): #sbml conversion into antimony str
sbmlloc, sedmlloc = manifestsearch(zipextloc)
sbml = te.readFromFile(zipextloc + sbmlloc)
sbmlantimony = te.sbmlToAntimony(sbml)
return sbmlantimony
def sbmlconv(zipextloc):
sbmlloc, sedmlloc = manifestsearch(zipextloc)
sbml = te.readFromFile(zipextloc + sbmlloc)
sbmlantimony = te.sbmlToAntimony(sbml)
return sbmlantimony
# Back to the main [Index](../index.ipynb)
# ### Test models
# 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
# To get the builtin models use listTestModels
print(te.listTestModels())
# #### Load test model
# In[2]:
# To load one of the test models use loadTestModel:
# r = te.loadTestModel('feedback.xml')
# result = r.simulate (0, 10, 100)
# r.plot (result)
# If you need to obtain the SBML for the test model, use getTestModel
sbml = te.getTestModel('feedback.xml')
# To look at one of the test model in Antimony form:
ant = te.sbmlToAntimony(te.getTestModel('feedback.xml'))
print(ant)
def translate(combine, filename):
tempPath = [[]]
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
rePath = r"(\w*).load\('(.*)'\)"
reLoad = r"(\w*) = roadrunner.RoadRunner\(\)"
reSelections = r'(\w+)\.selections = \[(.*),?\]'
outputstr = "# -*- coding: utf-8 -*-\n\n" + '"Generated by Import Combine plugin ' + time.strftime(
"%m/%d/%Y"
) + '"\n"Extracted from ' + filename + '"\n\n# Translated SBML\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = se.sedml_to_python(zipextloc + sedmlloclist[j])
lines = sedmlstr.splitlines()
for i, s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
modpath = getbasename(reSearchPath[2])[:-4].replace(
'-', '_')
if modpath[0].isdigit() == True:
modpath = 'Model_' + modpath
tempPath.append([reSearchPath[1], modpath])
else:
tempPath.append([reSearchPath[1], modpath])
#if '.xml' in s:
del lines[i]
for i, s in enumerate(lines):
reSearchLoad = re.split(reLoad, s)
if len(reSearchLoad) > 1:
for k in range(len(tempPath) - 1):
if reSearchLoad[1] == tempPath[k + 1][0]:
s = s.replace(
"roadrunner.RoadRunner()",
"te.loada(" + str(tempPath[k + 1][1]) + ")")
lines[i] = s
#if '"compartment"' or "'compartment'" in sedmlstr:
# reSearchSelections = re.split(reSelections, s)
# if len(reSearchSelections) > 1:
# Vars = reSearchSelections[2].replace(' ','').split(',')
# Vars = [s.replace('"','') for s in Vars]
# for i in range(len(Vars)):
# if Vars[i] == "compartment":
# Vars[i] = "compartment_"
if not "import tellurium" in sedmlstr:
if "import roadrunner" in sedmlstr:
for i, s in enumerate(lines):
if "import roadrunner" in s:
del lines[i]
lines.insert(i, "import tellurium as te")
else:
pass
else:
outputstr = outputstr + "import tellurium as te\n\n"
sedmlstr = '\n'.join(lines)
# List of replacements
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(outputstr + tempPath[1][1] + " = '''\n" +
sbmlstrlist[0] + "'''\n\n" + sedmlstrlist[k])
delseq(zipextloc)
return outputstrlist
def getAntimony(self):
'''
Returns antimony representation of model
'''
import tellurium as te
return te.sbmlToAntimony(self.getSbml())
