diff --git a/.gitignore b/.gitignore
index 88e84a6..e33861b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,6 @@ x86_64
/__pycache__
.DS_Store
/NeuroML/*.dat
+/NeuroML/report.*.txt
+/NeuroML/IClamp_AIY.json
+/NeuroML/Sim_IClamp_AIY.json
diff --git a/NeuroML/AIY.cell.nml b/NeuroML/AIY.cell.nml
new file mode 100644
index 0000000..963d376
--- /dev/null
+++ b/NeuroML/AIY.cell.nml
@@ -0,0 +1,32 @@
+
+ A cell from Nicoletti et al. 2019
+
+ |
+ AIY cell from Nicoletti et al. 2019
+
+
+
+
+
+
+ Default soma segment group for the cell
+
+
+
+ Default segment group for all segments in the cell
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ |
+
diff --git a/NeuroML/GenerateNeuroML.py b/NeuroML/GenerateNeuroML.py
new file mode 100644
index 0000000..cc291ec
--- /dev/null
+++ b/NeuroML/GenerateNeuroML.py
@@ -0,0 +1,251 @@
+from neuroml import NeuroMLDocument
+from neuroml.utils import component_factory
+
+from pyneuroml import pynml
+from pyneuroml.xppaut import parse_script
+from pprint import pprint
+
+from neuroml import GateHHRates
+from neuroml import IncludeType
+import sympy
+from sympy.parsing.sympy_parser import parse_expr
+import math
+
+
+colors = {"AIY": "0.8 0 0"}
+
+conductances = [
+ "leak",
+ "slo1iso",
+ "kqt1",
+ "egl19",
+ "slo1egl19",
+ "nca",
+ "irk",
+ "eleak",
+ "cm",
+]
+g0 = [0.14, 1, 0.2, 0.1, 0.92, 0.06, 0.5, -89.57, 1.6]
+
+cell_params = {}
+
+cell = "AIY"
+cell_params[cell] = {}
+for a in zip(conductances, g0):
+ print(f"Setting {a[0]} = {a[1]} for {cell}")
+ cell_params[cell][a[0]] = a[1]
+
+
+def generate_nmllite(
+ cell,
+ duration=700,
+ config="IClamp",
+ parameters=None,
+ stim_delay=310,
+ stim_duration=500,
+ channels_to_include=[],
+):
+ from neuromllite import Cell, InputSource
+
+ # from neuromllite.NetworkGenerator import *
+ from neuromllite.utils import create_new_model
+
+ reference = "%s_%s" % (config, cell)
+
+ cell_id = "%s" % cell
+ cell_nmll = Cell(id=cell_id, neuroml2_source_file="%s.cell.nml" % (cell))
+
+ ################################################################################
+ ### Add some inputs
+
+ if "IClamp" in config:
+ if not parameters:
+ parameters = {}
+ parameters["stim_amp"] = "10pA"
+ parameters["stim_delay"] = "%sms" % stim_delay
+ parameters["stim_duration"] = "%sms" % stim_duration
+
+ input_source = InputSource(
+ id="iclamp_0",
+ neuroml2_input="PulseGenerator",
+ parameters={
+ "amplitude": "stim_amp",
+ "delay": "stim_delay",
+ "duration": "stim_duration",
+ },
+ )
+
+ else:
+ if not parameters:
+ parameters = {}
+ parameters["average_rate"] = "100 Hz"
+ parameters["number_per_cell"] = "10"
+
+ input_source = InputSource(
+ id="pfs0",
+ neuroml2_input="PoissonFiringSynapse",
+ parameters={
+ "average_rate": "average_rate",
+ "synapse": syn_exc.id,
+ "spike_target": "./%s" % syn_exc.id,
+ },
+ )
+
+ sim, net = create_new_model(
+ reference,
+ duration,
+ dt=0.025, # ms
+ temperature=34, # degC
+ default_region="Worm",
+ parameters=parameters,
+ cell_for_default_population=cell_nmll,
+ color_for_default_population=colors[cell],
+ input_for_default_population=input_source,
+ )
+ sim.record_variables = {"caConc": {"all": "*"}}
+ for c in channels_to_include:
+ not_on_rmd = ["kvs1", "kqt3", "egl2"]
+ if c == "ca":
+ c = "sk"
+
+ if c != "egl36" and cell != "AWCon" and not (c in not_on_rmd and cell == "RMD"):
+ sim.record_variables["biophys/membraneProperties/%s_chans/gDensity" % c] = {
+ "all": "*"
+ }
+ sim.record_variables["biophys/membraneProperties/%s_chans/iDensity" % c] = {
+ "all": "*"
+ }
+ if (
+ c != "leak"
+ and c != "nca"
+ and not (c == "egl36" and cell == "AWCon")
+ and not (c in not_on_rmd and cell == "RMD")
+ ):
+ sim.record_variables[
+ "biophys/membraneProperties/%s_chans/%s_%s/m/q" % (c, cell, c)
+ ] = {"all": "*"}
+ if (
+ c != "leak"
+ and c not in ["nca", "kir", "sk", "egl36", "kqt3", "egl2"]
+ and not (c in not_on_rmd and cell == "RMD")
+ ):
+ sim.record_variables[
+ "biophys/membraneProperties/%s_chans/%s_%s/h/q" % (c, cell, c)
+ ] = {"all": "*"}
+
+ if cell == "AWCon" and c in ["kqt3"]:
+ sim.record_variables[
+ "biophys/membraneProperties/%s_chans/%s_%s/s/q" % (c, cell, c)
+ ] = {"all": "*"}
+ sim.record_variables[
+ "biophys/membraneProperties/%s_chans/%s_%s/w/q" % (c, cell, c)
+ ] = {"all": "*"}
+
+ sim.to_json_file()
+
+ return sim, net
+
+
+def create_cells(channels_to_include, duration=700, stim_delay=310, stim_duration=500):
+ for cell_id in cell_params.keys():
+ # Create the nml file and add the ion channels
+ cell_doc = NeuroMLDocument(
+ id=cell_id, notes="A cell from Nicoletti et al. 2019"
+ )
+ cell_fn = "%s.cell.nml" % cell_id
+
+ # Define a cell
+ cell = cell_doc.add(
+ "Cell", id=cell_id, notes="%s cell from Nicoletti et al. 2019" % cell_id
+ )
+ """
+ volume_um3 = xpps[cell_id]["parameters"]["vol"]
+ diam = 1.7841242
+ end_area = math.pi * diam * diam / 4
+ length = volume_um3 / end_area
+ surface_area_curved = length * math.pi * diam"""
+
+ surf = 65.89e-8 # surface in cm^2 form neuromorpho AIYL
+ vol = 7.42e-12 # total volume
+ L = math.sqrt(surf / math.pi)
+ rsoma = L * 1e4
+
+ cell.add_segment(
+ prox=[0, 0, 0, rsoma * 2],
+ dist=[0, rsoma * 2, 0, rsoma * 2],
+ name="soma",
+ parent=None,
+ fraction_along=1.0,
+ seg_type="soma",
+ )
+
+ cell.add_membrane_property("SpikeThresh", value="0mV")
+
+ cell.set_specific_capacitance("%s F_per_m2" % (cell_params[cell_id]["cm"]))
+
+ cell.set_init_memb_potential("-70mV")
+
+ # This value is not really used as it's a single comp cell model
+ cell.set_resistivity("0.1 kohm_cm")
+
+ density_factor = 1
+
+ for channel_id in channels_to_include:
+ print(cell_params[cell_id])
+ cell.add_channel_density(
+ cell_doc,
+ cd_id="%s_chans" % channel_id,
+ cond_density="%s S_per_m2" % cell_params[cell_id][channel_id],
+ erev="%smV" % cell_params[cell_id]["eleak"],
+ ion="non_specific",
+ ion_channel="%s" % channel_id,
+ ion_chan_def_file="%s.channel.nml" % channel_id,
+ )
+
+ """
+ cell_doc.includes.append(IncludeType(href="CaDynamics.nml"))
+ #
+ species = component_factory(
+ "Species",
+ id="ca",
+ ion="ca",
+ concentration_model="CaDynamics_%s" % cell_id,
+ initial_concentration="5e-5 mM",
+ initial_ext_concentration="2 mM",
+ )
+
+ cell.biophysical_properties.intracellular_properties.add(species)"""
+
+ cell.info(show_contents=True)
+
+ cell_doc.validate(recursive=True)
+ pynml.write_neuroml2_file(
+ nml2_doc=cell_doc, nml2_file_name=cell_fn, validate=True
+ )
+
+ sim, net = generate_nmllite(
+ cell_id,
+ duration=duration,
+ config="IClamp",
+ parameters=None,
+ stim_delay=stim_delay,
+ stim_duration=stim_duration,
+ channels_to_include=channels_to_include,
+ )
+
+ ################################################################################
+ ### Run in some simulators
+
+ from neuromllite.NetworkGenerator import check_to_generate_or_run
+ import sys
+
+ check_to_generate_or_run(sys.argv, sim)
+
+
+if __name__ == "__main__":
+ create_cells(
+ channels_to_include=["leak"],
+ duration=400,
+ stim_delay=100,
+ stim_duration=200,
+ )
diff --git a/NeuroML/IClamp_AIY.net.nml b/NeuroML/IClamp_AIY.net.nml
new file mode 100644
index 0000000..e1c8a96
--- /dev/null
+++ b/NeuroML/IClamp_AIY.net.nml
@@ -0,0 +1,26 @@
+
+ Generated by NeuroMLlite v0.6.0
+ Generated network: IClamp_AIY
+ Generation seed: 1234
+ NeuroMLlite parameters:
+ stim_amp = 10pA
+ stim_delay = 100ms
+ stim_duration = 200ms
+
+
+
+ A network model: IClamp_AIY
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/NeuroML/LEMS_Sim_IClamp_AIY.xml b/NeuroML/LEMS_Sim_IClamp_AIY.xml
new file mode 100644
index 0000000..3f387fb
--- /dev/null
+++ b/NeuroML/LEMS_Sim_IClamp_AIY.xml
@@ -0,0 +1,56 @@
+
+
+
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+
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diff --git a/NeuroML/clean.sh b/NeuroML/clean.sh
new file mode 100755
index 0000000..1707ecd
--- /dev/null
+++ b/NeuroML/clean.sh
@@ -0,0 +1 @@
+mv *dat *txt LEMS_Test*.xml *.mod *nrn.py *.hoc /tmp
diff --git a/NeuroML/leak.channel.nml b/NeuroML/leak.channel.nml
new file mode 100644
index 0000000..0ff4bee
--- /dev/null
+++ b/NeuroML/leak.channel.nml
@@ -0,0 +1,6 @@
+
+ An ion channel from Nicoletti et al. 2024
+
+ leak channel from Nicoletti et al. 2024
+
+
diff --git a/NeuroML/regenerateAndTest.sh b/NeuroML/regenerateAndTest.sh
new file mode 100755
index 0000000..f3e63b2
--- /dev/null
+++ b/NeuroML/regenerateAndTest.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+set -ex
+
+# Format the code
+black *.py
+
+python GenerateNeuroML.py -jnml
+
+
+omv all -V
+