Ex2: Izhikevich

Izhikevich 2003 spiking neuron — tonic, bursting, mixed, and class-1 modes

Model: Izhikevich 2003

The Izhikevich (2003) model is a computationally efficient spiking neuron with four firing modes from different parameter sets.

Reference: NeuroML2 LEMS_NML2_Ex2_Izh.xml

---

1. Define Network in TVBO

from tvbo import SimulationExperiment

exp = SimulationExperiment.from_string("""
label: "NeuroML Ex2: Izhikevich"
dynamics:
  name: izBurst
  iri: neuroml:izhikevichCell
network:
  dynamics:
    izBurst:
      name: izBurst
      iri: neuroml:izhikevichCell
      parameters:
        v0: {value: -70, unit: mV}
        thresh: {value: 30, unit: mV}
        a: {value: 0.02}
        b: {value: 0.2}
        c: {value: -50}
        d: {value: 2}
    izTonic:
      name: izTonic
      iri: neuroml:izhikevichCell
      parameters:
        v0: {value: -70, unit: mV}
        thresh: {value: 30, unit: mV}
        a: {value: 0.02}
        b: {value: 0.2}
        c: {value: -65}
        d: {value: 6}
    izMixed:
      name: izMixed
      iri: neuroml:izhikevichCell
      parameters:
        v0: {value: -70, unit: mV}
        thresh: {value: 30, unit: mV}
        a: {value: 0.02}
        b: {value: 0.2}
        c: {value: -55}
        d: {value: 4}
    izClass1:
      name: izClass1
      iri: neuroml:izhikevichCell
      parameters:
        v0: {value: -60, unit: mV}
        thresh: {value: 30, unit: mV}
        a: {value: 0.02}
        b: {value: -0.1}
        c: {value: -55}
        d: {value: 6}
    i0:
      name: i0
      iri: neuroml:pulseGeneratorDL
      parameters:
        delay: {value: 22, unit: ms}
        duration: {value: 2000, unit: ms}
        amplitude: {value: 15}
    i1:
      name: i1
      iri: neuroml:pulseGeneratorDL
      parameters:
        delay: {value: 20, unit: ms}
        duration: {value: 2000, unit: ms}
        amplitude: {value: 14}
    i2:
      name: i2
      iri: neuroml:pulseGeneratorDL
      parameters:
        delay: {value: 20, unit: ms}
        duration: {value: 2000, unit: ms}
        amplitude: {value: 10}
    rg0:
      name: rg0
      iri: neuroml:rampGeneratorDL
      parameters:
        delay: {value: 30, unit: ms}
        duration: {value: 170, unit: ms}
        startAmplitude: {value: -32}
        finishAmplitude: {value: 50}
        baselineAmplitude: {value: -32}
  nodes:
    - {id: 0, dynamics: izBurst}
    - {id: 1, dynamics: izTonic}
    - {id: 2, dynamics: izMixed}
    - {id: 3, dynamics: izClass1}
    - {id: 10, dynamics: i0, record: false}
    - {id: 11, dynamics: i1, record: false}
    - {id: 12, dynamics: i2, record: false}
    - {id: 13, dynamics: rg0, record: false}
  edges:
    - {source: 10, target: 0}
    - {source: 11, target: 1}
    - {source: 12, target: 2}
    - {source: 13, target: 3}
integration:
  method: euler
  step_size: 0.005
  duration: 200.0
  time_scale: ms
""")
print(f"Network dynamics: {list(exp.network.dynamics.keys())}")

Network dynamics: ['i0', 'i1', 'i2', 'izBurst', 'izClass1', 'izMixed', 'izTonic', 'rg0']

2. Render LEMS XML

xml = exp.render("lems")
print(xml[:2000])

<Lems>
  <Target component="sim_NeuroML_Ex2__Izhikevich"/>

  <Include file="Cells.xml"/>
  <Include file="Networks.xml"/>
  <Include file="Inputs.xml"/>
  <Include file="Simulation.xml"/>

    <izhikevichCell id="izBurst" a="0.02" b="0.2" c="-50" d="2" thresh="30 mV" v0="-70 mV"/>

    <izhikevichCell id="izTonic" a="0.02" b="0.2" c="-65" d="6" thresh="30 mV" v0="-70 mV"/>

    <izhikevichCell id="izMixed" a="0.02" b="0.2" c="-55" d="4" thresh="30 mV" v0="-70 mV"/>

    <izhikevichCell id="izClass1" a="0.02" b="-0.1" c="-55" d="6" thresh="30 mV" v0="-60 mV"/>

    <pulseGeneratorDL id="i0" amplitude="15.0" delay="22.0 ms" duration="2000.0 ms"/>

    <pulseGeneratorDL id="i1" amplitude="14.0" delay="20.0 ms" duration="2000.0 ms"/>

    <pulseGeneratorDL id="i2" amplitude="10.0" delay="20.0 ms" duration="2000.0 ms"/>

    <rampGeneratorDL id="rg0" baselineAmplitude="-32.0" delay="30.0 ms" duration="170.0 ms" finishAmplitude="50.0" startAmplitude="-32.0"/>

    <network id="net1">
        <population id="izBurst_pop" component="izBurst" size="1"/>
        <population id="izTonic_pop" component="izTonic" size="1"/>
        <population id="izMixed_pop" component="izMixed" size="1"/>
        <population id="izClass1_pop" component="izClass1" size="1"/>
        <explicitInput target="izBurst_pop[0]" input="i0" destination="synapses"/>
        <explicitInput target="izTonic_pop[0]" input="i1" destination="synapses"/>
        <explicitInput target="izMixed_pop[0]" input="i2" destination="synapses"/>
        <explicitInput target="izClass1_pop[0]" input="rg0" destination="synapses"/>
    </network>

    <Simulation id="sim_NeuroML_Ex2__Izhikevich" length="200.0ms" step="0.005ms" target="net1">
        <OutputFile id="of0" fileName="results/izBurst.dat">
            <OutputColumn id="izBurst_pop_0_v" quantity="izBurst_pop[0]/v"/>
        </OutputFile>
        <OutputFile id="of1" fileName="results/izTonic.dat">
            <OutputColumn id="izTonic_pop_0_v" quantity="izTonic_

3. Run Reference

from tvbo.adapters.neuroml import run_lems_example

ref_outputs = run_lems_example("LEMS_NML2_Ex2_Izh.xml")
for name, arr in ref_outputs.items():
    print(f"  {name}: shape={arr.shape}")

  auto.dat: shape=(40001, 10)

4. Run TVBO

result = exp.run("neuroml")
da = result.integration.data
print(f"TVBO: {da.dims}, shape={da.shape}")

TVBO: ('time', 'quantity'), shape=(40001, 4)

5. Compare & Plot

from tvbo.adapters.neuroml import plot_lems_comparison
plot_lems_comparison("LEMS_NML2_Ex2_Izh.xml", ref_outputs, result.integration.data, title_prefix="Ex2")