Examples¶
The examples in this section are intended to give in depth overviews of how to accomplish specific tasks with libNeuroML.
These examples are located in the neuroml/examples directory and can be tested to confirm they work by running the run_all.py script.
Examples
Creating a NeuroML morphology¶
"""
Example of connecting segments together to create a
multicompartmental model of a cell.
"""
import neuroml
import neuroml.writers as writers
p = neuroml.Point3DWithDiam(x=0,y=0,z=0,diameter=50)
d = neuroml.Point3DWithDiam(x=50,y=0,z=0,diameter=50)
soma = neuroml.Segment(proximal=p, distal=d)
soma.name = 'Soma'
soma.id = 0
# Make an axon with 100 compartments:
parent = neuroml.SegmentParent(segments=soma.id)
parent_segment = soma
axon_segments = []
seg_id = 1
for i in range(100):
p = neuroml.Point3DWithDiam(x=parent_segment.distal.x,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
d = neuroml.Point3DWithDiam(x=parent_segment.distal.x+10,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
axon_segment = neuroml.Segment(proximal = p,
distal = d,
parent = parent)
axon_segment.id = seg_id
axon_segment.name = 'axon_segment_' + str(axon_segment.id)
#now reset everything:
parent = neuroml.SegmentParent(segments=axon_segment.id)
parent_segment = axon_segment
seg_id += 1
axon_segments.append(axon_segment)
test_morphology = neuroml.Morphology()
test_morphology.segments.append(soma)
test_morphology.segments += axon_segments
test_morphology.id = "TestMorphology"
cell = neuroml.Cell()
cell.name = 'TestCell'
cell.id = 'TestCell'
cell.morphology = test_morphology
doc = neuroml.NeuroMLDocument(id = "TestNeuroMLDocument")
doc.cells.append(cell)
nml_file = 'tmp/testmorphwrite.nml'
writers.NeuroMLWriter.write(doc,nml_file)
print("Written morphology file to: "+nml_file)
###### Validate the NeuroML ######
from neuroml.utils import validate_neuroml2
validate_neuroml2(nml_file)
Loading and modifying a file¶
"""
In this example an axon is built, a morphology is loaded, the axon is
then connected to the loadeed morphology.
"""
import neuroml
import neuroml.loaders as loaders
import neuroml.writers as writers
fn = './test_files/Purk2M9s.nml'
doc = loaders.NeuroMLLoader.load(fn)
print("Loaded morphology file from: "+fn)
#get the parent segment:
parent_segment = doc.cells[0].morphology.segments[0]
parent = neuroml.SegmentParent(segments=parent_segment.id)
#make an axon:
seg_id = 5000 # need a way to get a unique id from a morphology
axon_segments = []
for i in range(10):
p = neuroml.Point3DWithDiam(x=parent_segment.distal.x,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
d = neuroml.Point3DWithDiam(x=parent_segment.distal.x+10,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
axon_segment = neuroml.Segment(proximal = p,
distal = d,
parent = parent)
axon_segment.id = seg_id
axon_segment.name = 'axon_segment_' + str(axon_segment.id)
#now reset everything:
parent = neuroml.SegmentParent(segments=axon_segment.id)
parent_segment = axon_segment
seg_id += 1
axon_segments.append(axon_segment)
doc.cells[0].morphology.segments += axon_segments
nml_file = './tmp/modified_morphology.nml'
writers.NeuroMLWriter.write(doc,nml_file)
print("Saved modified morphology file to: "+nml_file)
###### Validate the NeuroML ######
from neuroml.utils import validate_neuroml2
validate_neuroml2(nml_file)
Building a network¶
"""
Example to build a full spiking IaF network
through libNeuroML, save it as XML and validate it
"""
from neuroml import NeuroMLDocument
from neuroml import IafCell
from neuroml import Network
from neuroml import ExpOneSynapse
from neuroml import Population
from neuroml import PulseGenerator
from neuroml import ExplicitInput
from neuroml import SynapticConnection
import neuroml.writers as writers
from random import random
nml_doc = NeuroMLDocument(id="IafNet")
IafCell0 = IafCell(id="iaf0",
C="1.0 nF",
thresh = "-50mV",
reset="-65mV",
leak_conductance="10 nS",
leak_reversal="-65mV")
nml_doc.iaf_cells.append(IafCell0)
IafCell1 = IafCell(id="iaf1",
C="1.0 nF",
thresh = "-50mV",
reset="-65mV",
leak_conductance="20 nS",
leak_reversal="-65mV")
nml_doc.iaf_cells.append(IafCell1)
syn0 = ExpOneSynapse(id="syn0",
gbase="65nS",
erev="0mV",
tau_decay="3ms")
nml_doc.exp_one_synapses.append(syn0)
net = Network(id="IafNet")
nml_doc.networks.append(net)
size0 = 5
pop0 = Population(id="IafPop0",
component=IafCell0.id,
size=size0)
net.populations.append(pop0)
size1 = 5
pop1 = Population(id="IafPop1",
component=IafCell0.id,
size=size1)
net.populations.append(pop1)
prob_connection = 0.5
for pre in range(0,size0):
pg = PulseGenerator(id="pulseGen_%i"%pre,
delay="0ms",
duration="100ms",
amplitude="%f nA"%(0.1*random()))
nml_doc.pulse_generators.append(pg)
exp_input = ExplicitInput(target="%s[%i]"%(pop0.id,pre),
input=pg.id)
net.explicit_inputs.append(exp_input)
for post in range(0,size1):
# fromxx is used since from is Python keyword
if random() <= prob_connection:
syn = SynapticConnection(from_="%s[%i]"%(pop0.id,pre),
synapse=syn0.id,
to="%s[%i]"%(pop1.id,post))
net.synaptic_connections.append(syn)
nml_file = 'tmp/testnet.nml'
writers.NeuroMLWriter.write(nml_doc, nml_file)
print("Written network file to: "+nml_file)
###### Validate the NeuroML ######
from neuroml.utils import validate_neuroml2
validate_neuroml2(nml_file)
Building a 3D network¶
"""
Example to build a full spiking IaF network throught libNeuroML & save it as XML & validate it
"""
from neuroml import NeuroMLDocument
from neuroml import Network
from neuroml import ExpOneSynapse
from neuroml import Population
from neuroml import Property
from neuroml import Cell
from neuroml import Location
from neuroml import Instance
from neuroml import Morphology
from neuroml import Point3DWithDiam
from neuroml import Segment
from neuroml import SegmentParent
from neuroml import Projection
from neuroml import Connection
import neuroml.writers as writers
from random import random
soma_diam = 10
soma_len = 10
dend_diam = 2
dend_len = 10
dend_num = 10
def generateRandomMorphology():
morphology = Morphology()
p = Point3DWithDiam(x=0,y=0,z=0,diameter=soma_diam)
d = Point3DWithDiam(x=soma_len,y=0,z=0,diameter=soma_diam)
soma = Segment(proximal=p, distal=d, name = 'Soma', id = 0)
morphology.segments.append(soma)
parent_seg = soma
for dend_id in range(0,dend_num):
p = Point3DWithDiam(x=d.x,y=d.y,z=d.z,diameter=dend_diam)
d = Point3DWithDiam(x=p.x,y=p.y+dend_len,z=p.z,diameter=dend_diam)
dend = Segment(proximal=p, distal=d, name = 'Dend_%i'%dend_id, id = 1+dend_id)
dend.parent = SegmentParent(segments=parent_seg.id)
parent_seg = dend
morphology.segments.append(dend)
morphology.id = "TestMorphology"
return morphology
def run():
cell_num = 10
x_size = 500
y_size = 500
z_size = 500
nml_doc = NeuroMLDocument(id="Net3DExample")
syn0 = ExpOneSynapse(id="syn0", gbase="65nS", erev="0mV", tau_decay="3ms")
nml_doc.exp_one_synapses.append(syn0)
net = Network(id="Net3D")
nml_doc.networks.append(net)
proj_count = 0
#conn_count = 0
for cell_id in range(0,cell_num):
cell = Cell(id="Cell_%i"%cell_id)
cell.morphology = generateRandomMorphology()
nml_doc.cells.append(cell)
pop = Population(id="Pop_%i"%cell_id, component=cell.id, type="populationList")
net.populations.append(pop)
pop.properties.append(Property(tag="color", value="1 0 0"))
inst = Instance(id="0")
pop.instances.append(inst)
inst.location = Location(x=str(x_size*random()), y=str(y_size*random()), z=str(z_size*random()))
prob_connection = 0.5
for post in range(0,cell_num):
if post is not cell_id and random() <= prob_connection:
from_pop = "Pop_%i"%cell_id
to_pop = "Pop_%i"%post
pre_seg_id = 0
post_seg_id = 1
projection = Projection(id="Proj_%i"%proj_count, presynaptic_population=from_pop, postsynaptic_population=to_pop, synapse=syn0.id)
net.projections.append(projection)
connection = Connection(id=proj_count, \
pre_cell_id="%s[%i]"%(from_pop,0), \
pre_segment_id=pre_seg_id, \
pre_fraction_along=random(),
post_cell_id="%s[%i]"%(to_pop,0), \
post_segment_id=post_seg_id,
post_fraction_along=random())
projection.connections.append(connection)
proj_count += 1
#net.synaptic_connections.append(SynapticConnection(from_="%s[%i]"%(from_pop,0), to="%s[%i]"%(to_pop,0)))
####### Write to file ######
nml_file = 'tmp/net3d.nml'
writers.NeuroMLWriter.write(nml_doc, nml_file)
print("Written network file to: "+nml_file)
###### Validate the NeuroML ######
from neuroml.utils import validate_neuroml2
validate_neuroml2(nml_file)
run()
Ion channels¶
"""
Generating a Hodgkin-Huxley Ion Channel and writing it to NeuroML
"""
import neuroml
import neuroml.writers as writers
chan = neuroml.IonChannelHH(id='na',
conductance='10pS',
species='na',
notes="This is an example voltage-gated Na channel")
m_gate = neuroml.GateHHRates(id='m',instances='3')
h_gate = neuroml.GateHHRates(id='h',instances='1')
m_gate.forward_rate = neuroml.HHRate(type="HHExpRate",
rate="0.07per_ms",
midpoint="-65mV",
scale="-20mV")
m_gate.reverse_rate = neuroml.HHRate(type="HHSigmoidRate",
rate="1per_ms",
midpoint="-35mV",
scale="10mV")
h_gate.forward_rate = neuroml.HHRate(type="HHExpLinearRate",
rate="0.1per_ms",
midpoint="-55mV",
scale="10mV")
h_gate.reverse_rate = neuroml.HHRate(type="HHExpRate",
rate="0.125per_ms",
midpoint="-65mV",
scale="-80mV")
chan.gate_hh_rates.append(m_gate)
chan.gate_hh_rates.append(h_gate)
doc = neuroml.NeuroMLDocument()
doc.ion_channel_hhs.append(chan)
doc.id = "ChannelMLDemo"
nml_file = './tmp/ionChannelTest.xml'
writers.NeuroMLWriter.write(doc,nml_file)
print("Written channel file to: "+nml_file)
###### Validate the NeuroML ######
from neuroml.utils import validate_neuroml2
validate_neuroml2(nml_file)
PyNN models¶
"""
Example to build a PyNN based network
"""
from neuroml import NeuroMLDocument
from neuroml import *
import neuroml.writers as writers
from random import random
######################## Build the network ####################################
nml_doc = NeuroMLDocument(id="IafNet")
pynn0 = IF_curr_alpha(id="IF_curr_alpha_pop_IF_curr_alpha", cm="1.0", i_offset="0.9", tau_m="20.0", tau_refrac="10.0", tau_syn_E="0.5", tau_syn_I="0.5", v_init="-65", v_reset="-62.0", v_rest="-65.0", v_thresh="-52.0")
nml_doc.IF_curr_alpha.append(pynn0)
pynn1 = HH_cond_exp(id="HH_cond_exp_pop_HH_cond_exp", cm="0.2", e_rev_E="0.0", e_rev_I="-80.0", e_rev_K="-90.0", e_rev_Na="50.0", e_rev_leak="-65.0", g_leak="0.01", gbar_K="6.0", gbar_Na="20.0", i_offset="0.2", tau_syn_E="0.2", tau_syn_I="2.0", v_init="-65", v_offset="-63.0")
nml_doc.HH_cond_exp.append(pynn1)
pynnSynn0 = ExpCondSynapse(id="ps1", tau_syn="5", e_rev="0")
nml_doc.exp_cond_synapses.append(pynnSynn0)
nml_file = 'tmp/pynn_network.xml'
writers.NeuroMLWriter.write(nml_doc, nml_file)
print("Saved to: "+nml_file)
###### Validate the NeuroML ######
from neuroml.utils import validate_neuroml2
validate_neuroml2(nml_file)
Synapses¶
"""
Example to create a file with multiple synapse types
"""
from neuroml import NeuroMLDocument
from neuroml import *
import neuroml.writers as writers
from random import random
nml_doc = NeuroMLDocument(id="SomeSynapses")
expOneSyn0 = ExpOneSynapse(id="ampa", tau_decay="5ms", gbase="1nS", erev="0mV")
nml_doc.exp_one_synapses.append(expOneSyn0)
expTwoSyn0 = ExpTwoSynapse(id="gaba", tau_decay="12ms", tau_rise="3ms", gbase="1nS", erev="-70mV")
nml_doc.exp_two_synapses.append(expTwoSyn0)
bpSyn = BlockingPlasticSynapse(id="blockStpSynDep", gbase="1nS", erev="0mV", tau_rise="0.1ms", tau_decay="2ms")
bpSyn.notes = "This is a note"
bpSyn.plasticity_mechanism = PlasticityMechanism(type="tsodyksMarkramDepMechanism", init_release_prob="0.5", tau_rec="120 ms")
bpSyn.block_mechanism = BlockMechanism(type="voltageConcDepBlockMechanism", species="mg", block_concentration="1.2 mM", scaling_conc="1.920544 mM", scaling_volt="16.129 mV")
nml_doc.blocking_plastic_synapses.append(bpSyn)
nml_file = 'tmp/synapses.xml'
writers.NeuroMLWriter.write(nml_doc, nml_file)
print("Saved to: "+nml_file)
###### Validate the NeuroML ######
from neuroml.utils import validate_neuroml2
validate_neuroml2(nml_file)
Working with JSON serialization¶
One thing to note is that the JSONWriter, unlike NeuroMLWriter, will serializing using array-based (Arraymorph) representation if this has been used.
"""
In this example an axon is built, a morphology is loaded, the axon is
then connected to the loadeed morphology. The whole thing is serialized
in JSON format, reloaded and validated.
"""
import neuroml
import neuroml.loaders as loaders
import neuroml.writers as writers
fn = './test_files/Purk2M9s.nml'
doc = loaders.NeuroMLLoader.load(fn)
print("Loaded morphology file from: "+fn)
#get the parent segment:
parent_segment = doc.cells[0].morphology.segments[0]
parent = neuroml.SegmentParent(segments=parent_segment.id)
#make an axon:
seg_id = 5000 # need a way to get a unique id from a morphology
axon_segments = []
for i in range(10):
p = neuroml.Point3DWithDiam(x=parent_segment.distal.x,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
d = neuroml.Point3DWithDiam(x=parent_segment.distal.x+10,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
axon_segment = neuroml.Segment(proximal = p,
distal = d,
parent = parent)
axon_segment.id = seg_id
axon_segment.name = 'axon_segment_' + str(axon_segment.id)
#now reset everything:
parent = neuroml.SegmentParent(segments=axon_segment.id)
parent_segment = axon_segment
seg_id += 1
axon_segments.append(axon_segment)
doc.cells[0].morphology.segments += axon_segments
json_file = './tmp/modified_morphology.json'
writers.JSONWriter.write(doc,json_file)
print("Saved modified morphology in JSON format to: " + json_file)
##### load it again, this time write it to a normal neuroml file ###
neuroml_document_from_json = loaders.JSONLoader.load(json_file)
print("Re-loaded neuroml document in JSON format to NeuroMLDocument object")
nml_file = './tmp/modified_morphology_from_json.nml'
writers.NeuroMLWriter.write(neuroml_document_from_json,nml_file)
###### Validate the NeuroML ######
from neuroml.utils import validate_neuroml2
validate_neuroml2(nml_file)
Working with arraymorphs¶
"""
Example of connecting segments together to create a
multicompartmental model of a cell.
In this case ArrayMorphology will be used rather than
Morphology - demonstrating its similarity and
ability to save in HDF5 format
"""
import neuroml
import neuroml.writers as writers
import neuroml.arraymorph as am
p = neuroml.Point3DWithDiam(x=0,y=0,z=0,diameter=50)
d = neuroml.Point3DWithDiam(x=50,y=0,z=0,diameter=50)
soma = neuroml.Segment(proximal=p, distal=d)
soma.name = 'Soma'
soma.id = 0
#now make an axon with 100 compartments:
parent = neuroml.SegmentParent(segments=soma.id)
parent_segment = soma
axon_segments = []
seg_id = 1
for i in range(100):
p = neuroml.Point3DWithDiam(x=parent_segment.distal.x,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
d = neuroml.Point3DWithDiam(x=parent_segment.distal.x+10,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
axon_segment = neuroml.Segment(proximal = p,
distal = d,
parent = parent)
axon_segment.id = seg_id
axon_segment.name = 'axon_segment_' + str(axon_segment.id)
#now reset everything:
parent = neuroml.SegmentParent(segments=axon_segment.id)
parent_segment = axon_segment
seg_id += 1
axon_segments.append(axon_segment)
test_morphology = am.ArrayMorphology()
test_morphology.segments.append(soma)
test_morphology.segments += axon_segments
test_morphology.id = "TestMorphology"
cell = neuroml.Cell()
cell.name = 'TestCell'
cell.id = 'TestCell'
cell.morphology = test_morphology
doc = neuroml.NeuroMLDocument()
#doc.name = "Test neuroML document"
doc.cells.append(cell)
doc.id = "TestNeuroMLDocument"
nml_file = 'tmp/arraymorph.nml'
writers.NeuroMLWriter.write(doc,nml_file)
print("Written morphology file to: "+nml_file)
###### Validate the NeuroML ######
from neuroml.utils import validate_neuroml2
validate_neuroml2(nml_file)
Working with Izhikevich Cells¶
These examples were kindly contributed by Steve Marsh
#from neuroml import NeuroMLDocument
from neuroml import IzhikevichCell
from neuroml.loaders import NeuroMLLoader
from neuroml.utils import validate_neuroml2
def load_izhikevich(filename="./test_files/SingleIzhikevich.nml"):
nml_filename = filename
validate_neuroml2(nml_filename)
nml_doc = NeuroMLLoader.load(nml_filename)
iz_cells = nml_doc.izhikevich_cells
for i, iz in enumerate(iz_cells):
if isinstance(iz, IzhikevichCell):
neuron_string = "%d %s %s %s %s %s (%s)" % (i, iz.v0, iz.a, iz.b, iz.c, iz.d, iz.id)
print(neuron_string)
else:
print("Error: Cell %d is not an IzhikevichCell" % i)
load_izhikevich()
from neuroml import NeuroMLDocument
from neuroml import IzhikevichCell
from neuroml.writers import NeuroMLWriter
from neuroml.utils import validate_neuroml2
def write_izhikevich(filename="./tmp/SingleIzhikevich_test.nml"):
nml_doc = NeuroMLDocument(id="SingleIzhikevich")
nml_filename = filename
iz0 = IzhikevichCell(id="iz0", v0="-70mV", thresh="30mV", a="0.02", b="0.2", c="-65.0", d="6")
nml_doc.izhikevich_cells.append(iz0)
NeuroMLWriter.write(nml_doc, nml_filename)
validate_neuroml2(nml_filename)
write_izhikevich()
