def write(cfg, file_name):
""" Exports simulation configuration to SED-ML file
Args:
cfg (:obj:`WCSimulationConfig`): simulation configuration
file_name (:obj:`str`): path to write SED-ML file
"""
# initialize SED-ML document
cfg_ml = libsedml.SedDocument()
cfg_ml.setLevel(1)
cfg_ml.setVersion(2)
# write changes
mdl = cfg_ml.createModel()
for change in cfg.changes:
change_ml = mdl.createChangeAttribute()
change_ml.setTarget(change.attr_path_to_str())
change_ml.setNewValue(str(change.value))
# write perturbations
for perturbation in cfg.perturbations:
task_ml = cfg_ml.createRepeatedTask()
change_ml = task_ml.createTaskChange()
change_ml.setTarget(perturbation.change.attr_path_to_str())
change_ml.setMath(
libsedml.parseFormula(str(perturbation.change.value)))
if perturbation.end_time and not numpy.isnan(
perturbation.end_time):
range_ml = task_ml.createUniformRange()
range_ml.setStart(perturbation.start_time)
range_ml.setEnd(perturbation.end_time)
range_ml.setType('linear')
else:
range_ml = task_ml.createVectorRange()
range_ml.setValues([perturbation.start_time])
# simulation (maximum time, step size)
sim = cfg_ml.createUniformTimeCourse()
sim.setInitialTime(cfg.de_simulation_config.time_init)
sim.setOutputStartTime(cfg.de_simulation_config.time_init)
sim.setOutputEndTime(cfg.de_simulation_config.time_max)
duration = cfg.de_simulation_config.time_max - cfg.de_simulation_config.time_init
sim.setNumberOfPoints(int(duration / cfg.ode_time_step))
# simulation algorithm
alg = sim.createAlgorithm()
# .. todo:: add KISAO term for multi-algorithm method
alg.setKisaoID("KISAO_0000352") # hybrid method
# random number generator seed, state
if cfg.random_seed is not None:
param = alg.createAlgorithmParameter()
param.setKisaoID("KISAO_0000488")
param.setValue(str(cfg.random_seed))
# write to XML file
libsedml.writeSedML(cfg_ml, file_name)
def main(args):
"""Usage: echo_sedml input-filename output-filename
"""
if len(args) != 3:
print (main.__doc__)
sys.exit(1)
d = libsedml.readSedML(args[1])
if d.getErrorLog().getNumFailsWithSeverity(libsedml.LIBSEDML_SEV_ERROR) > 0:
print d.getErrorLog().toString()
else:
libsedml.writeSedML(d, args[2])
return 0
def main(args):
"""Usage: echo_sedml input-filename output-filename
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
d = libsedml.readSedML(args[1])
if (d.getErrorLog().getNumFailsWithSeverity(libsedml.LIBSEDML_SEV_ERROR) >
0):
print(d.getErrorLog().toString())
else:
libsedml.writeSedML(d, args[2])
return 0
def main (args):
"""Usage: create_sedml2 output-filename
"""
if (len(args) != 2):
print(main.__doc__)
sys.exit(1);
# create the document
doc = libsedml.SedDocument();
doc.setLevel(1);
doc.setVersion(3);
# create a data description
ddesc = doc.createDataDescription()
ddesc.setId('data1')
ddesc.setName('Oscli Timecourse data')
ddesc.setSource('foo.numl')
# create data source
dsource = ddesc.createDataSource()
dsource.setId('dataS1')
# create slice
slice = dsource.createSlice()
slice.setReference('SpeciesIds')
slice.setValue('S1')
# specify mapping
timeDesc = libsedml.CompositeDescription()
timeDesc.setIndexType('double')
timeDesc.setId('time')
timeDesc.setName('time')
speciesDesc = timeDesc.createCompositeDescription()
speciesDesc.setIndexType('string')
speciesDesc.setId('SpeciesIds')
speciesDesc.setName('SpeciesIds')
concentrationDesc = speciesDesc.createAtomicDescription()
concentrationDesc.setValueType("double")
concentrationDesc.setName("Concentrations")
dimDesc = ddesc.createDimensionDescription()
dimDesc.append(timeDesc)
# write the document
libsedml.writeSedML(doc, args[1]);
def main (args):
"""Usage: create_sedml output-filename
"""
if (len(args) != 2):
print(main.__doc__)
sys.exit(1);
# create the document
doc = libsedml.SedDocument();
doc.setLevel(1);
doc.setVersion(1);
# create a first model referencing an sbml file
model = doc.createModel();
model.setId("model1");
model.setSource("file.xml");
model.setLanguage("urn:sedml:language:sbml");
# create a second model modifying a variable of that other sbml file
model = doc.createModel();
model.setId("model2");
model.setSource("model1");
model.setLanguage("urn:sedml:sbml");
# change a paramerter 'k' to 0.1
change = model.createChangeAttribute();
change.setTarget("/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='k']/@value");
change.setNewValue("0.1");
# remove species 's1'
remove = model.createRemoveXML();
remove.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");
# now for something tricky we want to update the initialConcentration of 'S2' to be
# half what it was in the original model
compute = model.createComputeChange();
compute.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id="S2"]/@initialConcentration");
variable = compute.createVariable();
variable.setId("S2");
variable.setModelReference("model1");
variable.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S2']");
compute.setMath(libsedml.parseFormula("S2 / 2"));
# create simulation
tc = doc.createUniformTimeCourse();
tc.setId("sim1");
tc.setInitialTime(0.0);
tc.setOutputStartTime(0.0);
tc.setOutputEndTime(10.0);
tc.setNumberOfPoints(1000);
# need to set the correct KISAO Term
alg = tc.createAlgorithm();
alg.setKisaoID("KISAO:0000019");
# create a task that uses the simulation and the model above
task = doc.createTask();
task.setId("task1");
task.setModelReference("model1");
task.setSimulationReference("sim1");
# add a DataGenerator to hold the output for time
dg = doc.createDataGenerator();
dg.setId("time");
dg.setName("time");
var = dg.createVariable();
var.setId("v0");
var.setName("time");
var.setTaskReference("task1");
var.setSymbol("urn:sedml:symbol:time");
dg.setMath(libsedml.parseFormula("v0"));
# and one for S1
dg = doc.createDataGenerator();
dg.setId("S1");
dg.setName("S1");
var = dg.createVariable();
var.setId("v1");
var.setName("S1");
var.setTaskReference("task1");
var.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");
dg.setMath(libsedml.parseFormula("v1"));
# add a report
report = doc.createReport();
report.setId("r1");
report.setName("report 1");
set = report.createDataSet();
set.setId("ds1");
set.setLabel("time");
set.setDataReference("time");
set = report.createDataSet();
set.setId("ds2");
set.setLabel("S1");
set.setDataReference("S1");
# add a 2d plot
plot = doc.createPlot2D();
plot.setId("p1");
plot.setName("S1 Timecourse");
curve = plot.createCurve();
curve.setId("c1");
curve.setName("S1");
curve.setLogX(False);
curve.setLogY(False);
curve.setXDataReference("time");
curve.setYDataReference("S1");
# add a 3D Plot
plot2 = doc.createPlot3D();
plot2.setId("p2");
plot2.setName("dunno");
surf = plot2.createSurface();
surf.setId("surf1");
surf.setName("S1");
surf.setLogX(False);
surf.setLogY(False);
surf.setLogZ(False);
surf.setXDataReference("time");
surf.setYDataReference("S1");
surf.setZDataReference("S1");
# write the document
libsedml.writeSedML(doc, args[1]);
def main (args):
"""Usage: create_sedml output-filename
"""
if (len(args) != 2):
print(main.__doc__)
sys.exit(1);
# create the document
doc = libsedml.SedDocument();
doc.setLevel(1);
doc.setVersion(1);
# create a first model referencing an sbml file
model = doc.createModel();
model.setId("model1");
model.setSource("file.xml");
model.setLanguage("urn:sedml:sbml");
# create a second model modifying a variable of that other sbml file
model = doc.createModel();
model.setId("model2");
model.setSource("model1");
model.setLanguage("urn:sedml:sbml");
# change a paramerter 'k' to 0.1
change = model.createChangeAttribute();
change.setTarget("/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='k']/@value");
change.setNewValue("0.1");
# remove species 's1'
remove = model.createRemoveXML();
remove.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");
# now for something tricky we want to update the initialConcentration of 'S2' to be
# half what it was in the original model
compute = model.createComputeChange();
compute.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id="S2"]/@initialConcentration");
variable = compute.createVariable();
variable.setId("S2");
variable.setModelReference("model1");
variable.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S2']");
compute.setMath(libsedml.parseFormula("S2 / 2"));
# create simulation
tc = doc.createUniformTimeCourse();
tc.setId("sim1");
tc.setInitialTime(0.0);
tc.setOutputStartTime(0.0);
tc.setOutputEndTime(10.0);
tc.setNumberOfPoints(1000);
# need to set the correct KISAO Term
alg = tc.createAlgorithm();
alg.setKisaoID("KISAO:0000019");
# create a task that uses the simulation and the model above
task = doc.createTask();
task.setId("task1");
task.setModelReference("model1");
task.setSimulationReference("sim1");
# add a DataGenerator to hold the output for time
dg = doc.createDataGenerator();
dg.setId("time");
dg.setName("time");
var = dg.createVariable();
var.setId("v0");
var.setName("time");
var.setTaskReference("task1");
var.setSymbol("urn:sedml:symbol:time");
dg.setMath(libsedml.parseFormula("v0"));
# and one for S1
dg = doc.createDataGenerator();
dg.setId("S1");
dg.setName("S1");
var = dg.createVariable();
var.setId("v1");
var.setName("S1");
var.setTaskReference("task1");
var.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");
dg.setMath(libsedml.parseFormula("v1"));
# add a report
report = doc.createReport();
report.setId("r1");
report.setName("report 1");
set = report.createDataSet();
set.setId("ds1");
set.setLabel("time");
set.setDataReference("time");
set = report.createDataSet();
set.setId("ds2");
set.setLabel("S1");
set.setDataReference("S1");
# add a 2d plot
plot = doc.createPlot2D();
plot.setId("p1");
plot.setName("S1 Timecourse");
curve = plot.createCurve();
curve.setId("c1");
curve.setName("S1");
curve.setLogX(False);
curve.setLogY(False);
curve.setXDataReference("time");
curve.setYDataReference("S1");
# add a 3D Plot
plot2 = doc.createPlot3D();
plot2.setId("p2");
plot2.setName("dunno");
surf = plot2.createSurface();
surf.setId("surf1");
surf.setName("S1");
surf.setLogX(False);
surf.setLogY(False);
surf.setLogZ(False);
surf.setXDataReference("time");
surf.setYDataReference("S1");
surf.setZDataReference("S1");
# write the document
libsedml.writeSedML(doc, args[1]);
def create_sedml(filename,
simulator,
initial_time=0.0,
report_output_start=0.0,
report_output_end=10,
no_of_time_points=101):
# create the document
doc = libsedml.SedDocument()
doc.setLevel(1)
doc.setVersion(1)
# create a first model referencing an sbml file
model = doc.createModel()
model.setId(filename)
model.setSource(f'{filename}.xml')
model.setLanguage("urn:sedml:language:sbml")
# create simulation
# Hardcoding timepoints to its minimum
tc = doc.createUniformTimeCourse()
tc.setId(filename)
tc.setInitialTime(float(initial_time))
tc.setOutputStartTime(float(report_output_start))
tc.setOutputEndTime(float(report_output_end))
tc.setNumberOfPoints(int(no_of_time_points))
# need to set the correct KISAO Term
"""
VCell testing use CVODE KISAOID: 0000019
COPASI testing use LSODA KISAOID: 0000088
for basic testing
"""
alg = tc.createAlgorithm()
if simulator == 'copasi':
alg.setKisaoID(f'KISAO:0000088')
elif simulator == 'vcell':
alg.setKisaoID(f'KISAO:0000019')
else:
print(f"{simulator} is still not supported to generate the SED-ML")
# create a task that uses the simulation and the model above
task = doc.createTask()
task.setId(filename)
task.setName(filename)
task.setModelReference(filename)
task.setSimulationReference(filename)
# add a DataGenerator to hold the output for time
dg = doc.createDataGenerator()
dg.setId("time")
dg.setName("time")
var = dg.createVariable()
var.setId("time")
var.setName("time")
var.setTaskReference(filename)
var.setSymbol("urn:sedml:symbol:time")
dg.setMath(libsedml.parseFormula("time"))
full_sbml_path = os.path.join(model_files_path, f'{filename}.xml')
reader = libsbml.SBMLReader()
sbml_model_file = reader.readSBMLFromFile(full_sbml_path)
sbml = sbml_model_file.getModel()
specie_list = []
for species_sbml in sbml.getListOfSpecies():
species_id = species_sbml.getId()
specie_list.append(species_id)
# adding a DataGenerator to hold the output for all species from the model
for specie in specie_list:
# and for species
dg = doc.createDataGenerator()
dg.setId(f'{specie}')
dg.setName(f'{specie}')
var = dg.createVariable()
var.setId(f'{specie}')
var.setName(f'{specie}')
var.setTaskReference(filename)
var.setTarget(
f"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='{specie}']"
)
dg.setMath(libsedml.parseFormula(f"{specie}"))
# add a report
report = doc.createReport()
report.setId(filename)
report.setName(filename)
set = report.createDataSet()
set.setId("time")
set.setLabel("time")
set.setDataReference("time")
for specie in specie_list:
set = report.createDataSet()
set.setId(f'{specie}')
set.setLabel(f'{specie}')
set.setDataReference(f'{specie}')
# write the document
libsedml.writeSedML(
doc, os.path.join(sedml_doc_path, simulator, f'{filename}.sedml'))
print(
f"SED-ML Document created for {simulator} with filename {filename}.sedml"
)
