Ex21: Current-Based Synapses

Current-based (as opposed to conductance-based) synaptic models

Model: Current-Based Synapses

Current-based synapses inject a fixed current waveform (alpha kernel) on spike arrival, independent of membrane voltage. Uses iafRefCell (IaF with refractory period) and alphaCurrentSynapse with spikeArray input.

Reference: NeuroML2 LEMS_NML2_Ex21_CurrentBasedSynapses.xml

1. Define Network in TVBO

from tvbo import SimulationExperiment

exp = SimulationExperiment.from_string("""
label: "NeuroML Ex21: IaF with Current-Based Synapses"
dynamics:
  name: iafRefCell
  iri: neuroml:iafRefCell
network:
  dynamics:
    iaf:
      name: iaf
      iri: neuroml:iafRefCell
      parameters:
        C: {value: 250, unit: pF}
        thresh: {value: 1, unit: mV}
        reset: {value: -1, unit: mV}
        leakConductance: {value: 12.5, unit: nS}
        leakReversal: {value: 0, unit: mV}
        refract: {value: 2, unit: ms}
    spks:
      name: spks
      iri: neuroml:spikeArray
      events:
        spikes:
          event_type: preset_time
          trigger_times: [100, 120, 126, 135]
  nodes:
    - {id: 0, dynamics: iaf}
    - {id: 1, dynamics: spks}
  edges:
    - source: 1
      target: 0
      coupling: alphaCurrentSynapse
      parameters:
        tau: {value: 1.0, unit: ms}
        ibase: {value: 1, unit: nA}
        weight: {value: 0.05}
        delay: {value: 1, unit: ms}
integration:
  method: euler
  step_size: 0.001
  duration: 300.0
  time_scale: ms
""")
print(f"Model: {exp.dynamics.name if exp.dynamics else 'network'}")

Model: iafRefCell

* Owlready2 * Warning: ignoring cyclic subclass of/subproperty of, involving:
  http://uri.interlex.org/tgbugs/uris/readable/atlas/Space

2. Render LEMS XML

xml = exp.render("lems")
print(xml[:1500])

<Lems>

  <!-- Tell jLEMS/jNeuroML which component is the simulation entry point. -->
  <Target component="sim_NeuroML_Ex21__IaF_with_Current_Based_Synapses"/>

  <!-- ════════════════════════════════════════════════════════════════
       Standard NeuroML2 type includes for network mode.
       Provides all standard dimensions, units, synapse types, input
       types, network infrastructure, and simulation types.
       ════════════════════════════════════════════════════════════════ -->
  <Include file="Cells.xml"/>
  <Include file="Networks.xml"/>
  <Include file="Simulation.xml"/>

  <!-- ════════════════════════════════════════════════════════════════
       Dynamics ComponentType & Component instances
       ════════════════════════════════════════════════════════════════ -->


  <!-- ── ComponentType: iaf ── -->
  <ComponentType name="iaf" extends="baseCellMembPot">
    <Parameter name="C" dimension="capacitance"/>
    <Parameter name="leakConductance" dimension="conductance"/>
    <Parameter name="leakReversal" dimension="voltage"/>
    <Parameter name="refract" dimension="time"/>
    <Parameter name="reset" dimension="voltage"/>
    <Parameter name="thresh" dimension="voltage"/>
    <Constant name="SEC" dimension="time" value="1ms"/>
    <!-- Dynamically attached synapses/inputs from network connections -->
    <Attachments name="synapses" type="basePointCurrent"/>

    <Dynamics>
      <!-- ── Flat dynamics ── -->
      <OnStart>
      </OnStart>
    </Dynamics>

3. Run Reference

from tvbo.adapters.neuroml import run_lems_example

ref_outputs = run_lems_example("LEMS_NML2_Ex21_CurrentBasedSynapses.xml")
for name, arr in ref_outputs.items():
    print(f"  {name}: shape={arr.shape}")

  ex21_v.dat: shape=(300001, 2)

4. Run TVBO

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

pyNeuroML >>> 13:05:59 - INFO - Loading LEMS file: tvbo_lems_sim.xml and running with jNeuroML
pyNeuroML >>> 13:05:59 - INFO - Executing: (java -Xmx400M  -Djava.awt.headless=true -jar  "/Users/leonmartin_bih/tools/tvbo/.venv/lib/python3.12/site-packages/pyneuroml/utils/./../lib/jNeuroML-0.14.0-jar-with-dependencies.jar"  tvbo_lems_sim.xml  -nogui -I '') in directory: /var/folders/ym/9kw1g21j1nd7kwfn8c0z3st40000gn/T/tmpowqxpe6e
pyNeuroML >>> 13:06:00 - INFO - Command completed successfully!

TVBO: ('time', 'quantity'), shape=(300001, 1)

5. Compare & Plot

from tvbo.adapters.neuroml import plot_lems_comparison
plot_lems_comparison("LEMS_NML2_Ex21_CurrentBasedSynapses.xml", ref_outputs, result.integration.data, title_prefix="Ex21")