Merge pull request #1 from sanjayankur31/neuroml-ankur

Setup for NeuroML conversion
OpenSourceBrain · Apr 9, 2024 · f93e565 · f93e565
2 parents d2fa677 + 7532ea8
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diff --git a/README.md → NEURON/README.md b/README.md → NEURON/README.md
diff --git a/analysis/display_ggn_vm_deflection_vclamp.py → ...lysis/display_ggn_vm_deflection_vclamp.py b/analysis/display_ggn_vm_deflection_vclamp.py → ...lysis/display_ggn_vm_deflection_vclamp.py
diff --git a/analysis/fig_active_kc_distr.py → NEURON/analysis/fig_active_kc_distr.py b/analysis/fig_active_kc_distr.py → NEURON/analysis/fig_active_kc_distr.py
diff --git a/analysis/fig_flat_pn_excitation.py → NEURON/analysis/fig_flat_pn_excitation.py b/analysis/fig_flat_pn_excitation.py → NEURON/analysis/fig_flat_pn_excitation.py
diff --git a/analysis/fig_ggn_dep_gbar_corr_kc_spikes.py → ...alysis/fig_ggn_dep_gbar_corr_kc_spikes.py b/analysis/fig_ggn_dep_gbar_corr_kc_spikes.py → ...alysis/fig_ggn_dep_gbar_corr_kc_spikes.py
diff --git a/analysis/fig_ggn_hyperpolarization.py → NEURON/analysis/fig_ggn_hyperpolarization.py b/analysis/fig_ggn_hyperpolarization.py → NEURON/analysis/fig_ggn_hyperpolarization.py
diff --git a/analysis/fig_ggn_ig_vm.py → NEURON/analysis/fig_ggn_ig_vm.py b/analysis/fig_ggn_ig_vm.py → NEURON/analysis/fig_ggn_ig_vm.py
diff --git a/analysis/fig_kc_removal.py → NEURON/analysis/fig_kc_removal.py b/analysis/fig_kc_removal.py → NEURON/analysis/fig_kc_removal.py
diff --git a/analysis/fig_kc_removal_v2.py → NEURON/analysis/fig_kc_removal_v2.py b/analysis/fig_kc_removal_v2.py → NEURON/analysis/fig_kc_removal_v2.py
diff --git a/...s/fig_pn_kc_ggn_plot_noshift_const_inh.py → ...s/fig_pn_kc_ggn_plot_noshift_const_inh.py b/...s/fig_pn_kc_ggn_plot_noshift_const_inh.py → ...s/fig_pn_kc_ggn_plot_noshift_const_inh.py
diff --git a/analysis/fig_shifting_pn_ggn_vm.py → NEURON/analysis/fig_shifting_pn_ggn_vm.py b/analysis/fig_shifting_pn_ggn_vm.py → NEURON/analysis/fig_shifting_pn_ggn_vm.py
diff --git a/analysis/fig_supp_steady_pn_lognorm_syn.py → ...nalysis/fig_supp_steady_pn_lognorm_syn.py b/analysis/fig_supp_steady_pn_lognorm_syn.py → ...nalysis/fig_supp_steady_pn_lognorm_syn.py
diff --git a/analysis/frac_kcs_high_spiking.py → NEURON/analysis/frac_kcs_high_spiking.py b/analysis/frac_kcs_high_spiking.py → NEURON/analysis/frac_kcs_high_spiking.py
diff --git a/analysis/network_data_analysis.py → NEURON/analysis/network_data_analysis.py b/analysis/network_data_analysis.py → NEURON/analysis/network_data_analysis.py
diff --git a/analysis/plot_RM_RA_sweep_alphaL_to_LCA.py → ...nalysis/plot_RM_RA_sweep_alphaL_to_LCA.py b/analysis/plot_RM_RA_sweep_alphaL_to_LCA.py → ...nalysis/plot_RM_RA_sweep_alphaL_to_LCA.py
diff --git a/analysis/plot_active_kc_distr.py → NEURON/analysis/plot_active_kc_distr.py b/analysis/plot_active_kc_distr.py → NEURON/analysis/plot_active_kc_distr.py
diff --git a/analysis/plot_fixed_net_multi_trial.py → ...ON/analysis/plot_fixed_net_multi_trial.py b/analysis/plot_fixed_net_multi_trial.py → ...ON/analysis/plot_fixed_net_multi_trial.py
diff --git a/analysis/plot_ggn_vm_ts.py → NEURON/analysis/plot_ggn_vm_ts.py b/analysis/plot_ggn_vm_ts.py → NEURON/analysis/plot_ggn_vm_ts.py
diff --git a/analysis/plot_shifting_pn_const_syn.py → ...ON/analysis/plot_shifting_pn_const_syn.py b/analysis/plot_shifting_pn_const_syn.py → ...ON/analysis/plot_shifting_pn_const_syn.py
diff --git a/analysis/plot_shifting_pn_lognorm_syn.py → .../analysis/plot_shifting_pn_lognorm_syn.py b/analysis/plot_shifting_pn_lognorm_syn.py → .../analysis/plot_shifting_pn_lognorm_syn.py
diff --git a/analysis/pn_kc_ggn_analysis.py → NEURON/analysis/pn_kc_ggn_analysis.py b/analysis/pn_kc_ggn_analysis.py → NEURON/analysis/pn_kc_ggn_analysis.py
diff --git a/analysis/pn_kc_ggn_plot.py → NEURON/analysis/pn_kc_ggn_plot.py b/analysis/pn_kc_ggn_plot.py → NEURON/analysis/pn_kc_ggn_plot.py
diff --git a/analysis/pn_kc_ggn_plot_mpl.py → NEURON/analysis/pn_kc_ggn_plot_mpl.py b/analysis/pn_kc_ggn_plot_mpl.py → NEURON/analysis/pn_kc_ggn_plot_mpl.py
diff --git a/analysis/remove_high_firing_kcs.py → NEURON/analysis/remove_high_firing_kcs.py b/analysis/remove_high_firing_kcs.py → NEURON/analysis/remove_high_firing_kcs.py
diff --git a/analysis/remove_high_firing_kcs_2.py → NEURON/analysis/remove_high_firing_kcs_2.py b/analysis/remove_high_firing_kcs_2.py → NEURON/analysis/remove_high_firing_kcs_2.py
diff --git a/common/nhpp.py → NEURON/common/nhpp.py b/common/nhpp.py → NEURON/common/nhpp.py
diff --git a/mb/__init__.py → NEURON/mb/__init__.py b/mb/__init__.py → NEURON/mb/__init__.py
diff --git a/mb/cell_templates/GGN_20170309_sc.hoc → NEURON/mb/cell_templates/GGN_20170309_sc.hoc b/mb/cell_templates/GGN_20170309_sc.hoc → NEURON/mb/cell_templates/GGN_20170309_sc.hoc
diff --git a/mb/cell_templates/GGN_20170309_sc.swc → NEURON/mb/cell_templates/GGN_20170309_sc.swc b/mb/cell_templates/GGN_20170309_sc.swc → NEURON/mb/cell_templates/GGN_20170309_sc.swc
diff --git a/mb/cell_templates/kc_1_comp.hoc → NEURON/mb/cell_templates/kc_1_comp.hoc b/mb/cell_templates/kc_1_comp.hoc → NEURON/mb/cell_templates/kc_1_comp.hoc
diff --git a/mb/config.py → NEURON/mb/config.py b/mb/config.py → NEURON/mb/config.py
diff --git a/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_nas_at_6.3_degC.png b/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_nas_at_6.3_degC.png
diff --git a/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_nas_at_6.3_degC.png b/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_nas_at_6.3_degC.png
diff --git a/mb/mod/gradedsyn.mod → NEURON/mb/mod/gradedsyn.mod b/mb/mod/gradedsyn.mod → NEURON/mb/mod/gradedsyn.mod
diff --git a/mb/mod/izhigs.mod → NEURON/mb/mod/izhigs.mod b/mb/mod/izhigs.mod → NEURON/mb/mod/izhigs.mod
diff --git a/mb/mod/ka_wustenberg.mod → NEURON/mb/mod/ka_wustenberg.mod b/mb/mod/ka_wustenberg.mod → NEURON/mb/mod/ka_wustenberg.mod
diff --git a/mb/mod/kst_wustenberg.mod → NEURON/mb/mod/kst_wustenberg.mod b/mb/mod/kst_wustenberg.mod → NEURON/mb/mod/kst_wustenberg.mod
diff --git a/mb/mod/kv_wustenberg.mod → NEURON/mb/mod/kv_wustenberg.mod b/mb/mod/kv_wustenberg.mod → NEURON/mb/mod/kv_wustenberg.mod
diff --git a/mb/mod/naf_wustenberg.mod → NEURON/mb/mod/naf_wustenberg.mod b/mb/mod/naf_wustenberg.mod → NEURON/mb/mod/naf_wustenberg.mod
diff --git a/mb/mod/nas_wustenberg.mod → NEURON/mb/mod/nas_wustenberg.mod b/mb/mod/nas_wustenberg.mod → NEURON/mb/mod/nas_wustenberg.mod
diff --git a/mb/mod/vecevent.mod → NEURON/mb/mod/vecevent.mod b/mb/mod/vecevent.mod → NEURON/mb/mod/vecevent.mod
diff --git a/mb/network/__init__.py → NEURON/mb/network/__init__.py b/mb/network/__init__.py → NEURON/mb/network/__init__.py
diff --git a/mb/network/change_pn_spikes.py → NEURON/mb/network/change_pn_spikes.py b/mb/network/change_pn_spikes.py → NEURON/mb/network/change_pn_spikes.py
diff --git a/mb/network/config.yaml → NEURON/mb/network/config.yaml b/mb/network/config.yaml → NEURON/mb/network/config.yaml
diff --git a/mb/network/fixed_network_changing_stim.py → ...mb/network/fixed_network_changing_stim.py b/mb/network/fixed_network_changing_stim.py → ...mb/network/fixed_network_changing_stim.py
diff --git a/mb/network/ig.py → NEURON/mb/network/ig.py b/mb/network/ig.py → NEURON/mb/network/ig.py
diff --git a/mb/network/kc_ggn_feedback_dclamp.py → NEURON/mb/network/kc_ggn_feedback_dclamp.py b/mb/network/kc_ggn_feedback_dclamp.py → NEURON/mb/network/kc_ggn_feedback_dclamp.py
diff --git a/...etwork/kc_ggn_feedback_frequency_sweep.py → ...etwork/kc_ggn_feedback_frequency_sweep.py b/...etwork/kc_ggn_feedback_frequency_sweep.py → ...etwork/kc_ggn_feedback_frequency_sweep.py
diff --git a/mb/network/kc_ggn_nofeedback.py → NEURON/mb/network/kc_ggn_nofeedback.py b/mb/network/kc_ggn_nofeedback.py → NEURON/mb/network/kc_ggn_nofeedback.py
diff --git a/mb/network/pn_kc_ggn_network.py → NEURON/mb/network/pn_kc_ggn_network.py b/mb/network/pn_kc_ggn_network.py → NEURON/mb/network/pn_kc_ggn_network.py
diff --git a/mb/network/pn_output.py → NEURON/mb/network/pn_output.py b/mb/network/pn_output.py → NEURON/mb/network/pn_output.py
diff --git a/mb/network/tweak_template.py → NEURON/mb/network/tweak_template.py b/mb/network/tweak_template.py → NEURON/mb/network/tweak_template.py
diff --git a/mb/slurm/batch_run_remove_kcs_run.sh → NEURON/mb/slurm/batch_run_remove_kcs_run.sh b/mb/slurm/batch_run_remove_kcs_run.sh → NEURON/mb/slurm/batch_run_remove_kcs_run.sh
diff --git a/mb/slurm/circular_run/batch_run.sh → NEURON/mb/slurm/circular_run/batch_run.sh b/mb/slurm/circular_run/batch_run.sh → NEURON/mb/slurm/circular_run/batch_run.sh
diff --git a/...r_run/batch_run_remove_high_firing_kcs.sh → ...r_run/batch_run_remove_high_firing_kcs.sh b/...r_run/batch_run_remove_high_firing_kcs.sh → ...r_run/batch_run_remove_high_firing_kcs.sh
diff --git a/...rm/circular_run/remove_high_firing_kcs.py → ...rm/circular_run/remove_high_firing_kcs.py b/...rm/circular_run/remove_high_firing_kcs.py → ...rm/circular_run/remove_high_firing_kcs.py
diff --git a/...cular_run/run_fixed_net_dep_remove_kcs.sh → ...cular_run/run_fixed_net_dep_remove_kcs.sh b/...cular_run/run_fixed_net_dep_remove_kcs.sh → ...cular_run/run_fixed_net_dep_remove_kcs.sh
diff --git a/...cular_run/run_remove_kcs_dep_fixed_net.sh → ...cular_run/run_remove_kcs_dep_fixed_net.sh b/...cular_run/run_remove_kcs_dep_fixed_net.sh → ...cular_run/run_remove_kcs_dep_fixed_net.sh
diff --git a/mb/slurm/run_fixed_net_changing_stim.py → ...N/mb/slurm/run_fixed_net_changing_stim.py b/mb/slurm/run_fixed_net_changing_stim.py → ...N/mb/slurm/run_fixed_net_changing_stim.py
diff --git a/mb/slurm/run_fixed_net_dep_remove_kcs.sh → .../mb/slurm/run_fixed_net_dep_remove_kcs.sh b/mb/slurm/run_fixed_net_dep_remove_kcs.sh → .../mb/slurm/run_fixed_net_dep_remove_kcs.sh
diff --git a/mb/slurm/run_fixed_net_with_ig.sh → NEURON/mb/slurm/run_fixed_net_with_ig.sh b/mb/slurm/run_fixed_net_with_ig.sh → NEURON/mb/slurm/run_fixed_net_with_ig.sh
diff --git a/mb/slurm/run_fixed_network_changing_stim.sh → .../slurm/run_fixed_network_changing_stim.sh b/mb/slurm/run_fixed_network_changing_stim.sh → .../slurm/run_fixed_network_changing_stim.sh
diff --git a/mb/slurm/run_kc_ggn_feedback_amp_sweep.sh → ...mb/slurm/run_kc_ggn_feedback_amp_sweep.sh b/mb/slurm/run_kc_ggn_feedback_amp_sweep.sh → ...mb/slurm/run_kc_ggn_feedback_amp_sweep.sh
diff --git a/mb/slurm/run_kc_ggn_nofeedback_amp_sweep.sh → .../slurm/run_kc_ggn_nofeedback_amp_sweep.sh b/mb/slurm/run_kc_ggn_nofeedback_amp_sweep.sh → .../slurm/run_kc_ggn_nofeedback_amp_sweep.sh
diff --git a/mb/slurm/run_mb_net.sh → NEURON/mb/slurm/run_mb_net.sh b/mb/slurm/run_mb_net.sh → NEURON/mb/slurm/run_mb_net.sh
diff --git a/mb/slurm/run_remove_high_firing_kcs.sh → ...ON/mb/slurm/run_remove_high_firing_kcs.sh b/mb/slurm/run_remove_high_firing_kcs.sh → ...ON/mb/slurm/run_remove_high_firing_kcs.sh
diff --git a/mb/slurm/run_remove_kcs.sh → NEURON/mb/slurm/run_remove_kcs.sh b/mb/slurm/run_remove_kcs.sh → NEURON/mb/slurm/run_remove_kcs.sh
diff --git a/mb/slurm/run_remove_kcs_dep_simulation.sh → ...mb/slurm/run_remove_kcs_dep_simulation.sh b/mb/slurm/run_remove_kcs_dep_simulation.sh → ...mb/slurm/run_remove_kcs_dep_simulation.sh
diff --git a/mb/slurm/run_remove_kcs_run.py → NEURON/mb/slurm/run_remove_kcs_run.py b/mb/slurm/run_remove_kcs_run.py → NEURON/mb/slurm/run_remove_kcs_run.py
diff --git a/mb/slurm/run_remove_kcs_run.sh → NEURON/mb/slurm/run_remove_kcs_run.sh b/mb/slurm/run_remove_kcs_run.sh → NEURON/mb/slurm/run_remove_kcs_run.sh
diff --git a/mb/slurm/run_to_reproduce_ggn_vm.sh → NEURON/mb/slurm/run_to_reproduce_ggn_vm.sh b/mb/slurm/run_to_reproduce_ggn_vm.sh → NEURON/mb/slurm/run_to_reproduce_ggn_vm.sh
diff --git a/mb/slurm/run_to_reproduce_ggn_vm_no_seed.sh → .../slurm/run_to_reproduce_ggn_vm_no_seed.sh b/mb/slurm/run_to_reproduce_ggn_vm_no_seed.sh → .../slurm/run_to_reproduce_ggn_vm_no_seed.sh
diff --git a/...n_to_reproduce_ggn_vm_with_shifting_pn.sh → ...n_to_reproduce_ggn_vm_with_shifting_pn.sh b/...n_to_reproduce_ggn_vm_with_shifting_pn.sh → ...n_to_reproduce_ggn_vm_with_shifting_pn.sh
diff --git a/mb/slurm/run_with_ig.sh → NEURON/mb/slurm/run_with_ig.sh b/mb/slurm/run_with_ig.sh → NEURON/mb/slurm/run_with_ig.sh
diff --git a/...st_cell/ggn_voltage_attenuation_vclamp.py → ...st_cell/ggn_voltage_attenuation_vclamp.py b/...st_cell/ggn_voltage_attenuation_vclamp.py → ...st_cell/ggn_voltage_attenuation_vclamp.py
diff --git a/mb/test_cell/run_param_sweep_vclamp.py → ...ON/mb/test_cell/run_param_sweep_vclamp.py b/mb/test_cell/run_param_sweep_vclamp.py → ...ON/mb/test_cell/run_param_sweep_vclamp.py
diff --git a/morphutils/cellmovie.py → NEURON/morphutils/cellmovie.py b/morphutils/cellmovie.py → NEURON/morphutils/cellmovie.py
diff --git a/morphutils/displaycell.py → NEURON/morphutils/displaycell.py b/morphutils/displaycell.py → NEURON/morphutils/displaycell.py
diff --git a/morphutils/morph3d.py → NEURON/morphutils/morph3d.py b/morphutils/morph3d.py → NEURON/morphutils/morph3d.py
diff --git a/morphutils/morph3d_vispy.py → NEURON/morphutils/morph3d_vispy.py b/morphutils/morph3d_vispy.py → NEURON/morphutils/morph3d_vispy.py
diff --git a/morphutils/morph3d_vpython.py → NEURON/morphutils/morph3d_vpython.py b/morphutils/morph3d_vpython.py → NEURON/morphutils/morph3d_vpython.py
diff --git a/morphutils/morph3d_vtk.py → NEURON/morphutils/morph3d_vtk.py b/morphutils/morph3d_vtk.py → NEURON/morphutils/morph3d_vtk.py
diff --git a/morphutils/morphoplot.py → NEURON/morphutils/morphoplot.py b/morphutils/morphoplot.py → NEURON/morphutils/morphoplot.py
diff --git a/morphutils/neurograph.py → NEURON/morphutils/neurograph.py b/morphutils/neurograph.py → NEURON/morphutils/neurograph.py
diff --git a/nrn/display_celltemplate.py → NEURON/nrn/display_celltemplate.py b/nrn/display_celltemplate.py → NEURON/nrn/display_celltemplate.py
diff --git a/nrn/ephys.py → NEURON/nrn/ephys.py b/nrn/ephys.py → NEURON/nrn/ephys.py
diff --git a/nrn/localized_input_output.py → NEURON/nrn/localized_input_output.py b/nrn/localized_input_output.py → NEURON/nrn/localized_input_output.py
diff --git a/nrn/localized_input_output_passive_sweep.py → ...n/localized_input_output_passive_sweep.py b/nrn/localized_input_output_passive_sweep.py → ...n/localized_input_output_passive_sweep.py
diff --git a/nrn/nrninit.bat → NEURON/nrn/nrninit.bat b/nrn/nrninit.bat → NEURON/nrn/nrninit.bat
diff --git a/nrn/nrninit.sh → NEURON/nrn/nrninit.sh b/nrn/nrninit.sh → NEURON/nrn/nrninit.sh
diff --git a/nrn/nrnutils.py → NEURON/nrn/nrnutils.py b/nrn/nrnutils.py → NEURON/nrn/nrnutils.py
diff --git a/nrn/plot_data_staggered_input.py → NEURON/nrn/plot_data_staggered_input.py b/nrn/plot_data_staggered_input.py → NEURON/nrn/plot_data_staggered_input.py
diff --git a/nrn/plot_localized_input_param_sweep.py → ...N/nrn/plot_localized_input_param_sweep.py b/nrn/plot_localized_input_param_sweep.py → ...N/nrn/plot_localized_input_param_sweep.py
diff --git a/nrn/staggered_input.py → NEURON/nrn/staggered_input.py b/nrn/staggered_input.py → NEURON/nrn/staggered_input.py
diff --git a/NeuroML2/GGN.cell.nml b/NeuroML2/GGN.cell.nml
diff --git a/NeuroML2/GGN.morph.cell.nml b/NeuroML2/GGN.morph.cell.nml
diff --git a/NeuroML2/Readme.md b/NeuroML2/Readme.md
@@ -0,0 +1,3 @@
+# NeuroML2
+
+NeuroML conversion of model: WIP
diff --git a/NeuroML2/channels/nas.channel.nml b/NeuroML2/channels/nas.channel.nml
@@ -0,0 +1,137 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="NeuroML_ionChannel">
+
+    <notes>NeuroML file containing a single ion channel</notes>
+
+    <ionChannel id="Navp" conductance="1pS" type="ionChannelHH" species="na">
+
+        <notes>
+            Implementation of slow Na+ channel ( NAS ) from Wustenberg DG, Boytcheva M, Grunewald B, Byrne JH, Menzel R, Baxter DA
+
+            This is slow Na+ channel in Apis mellifera Kenyon cells :(cultured).
+        </notes>
+
+        <gate id="m" type="gateHHratesTau" instances="3">
+            <forwardRate type="HHExpLinearRate" rate="1per_ms" midpoint="-30.1mV" scale="6.65mV"/>
+            <timeCourse type="Ray_nas_taum"/>
+        </gate>
+
+        <gate id="h" type="gateHHratesTau" instances="1">
+            <forwardRate type="HHExpLinearRate" rate="1per_ms" midpoint="-51.4mV" scale="5.9mV"/>
+            <timeCourse type="Ray_nas_tauh"/>
+        </gate>
+
+    </ionChannel>
+
+     <ComponentType name="Ray_nas_taum"
+                   extends="baseVoltageDepTime"
+                   description="Tau parameter to describe Navp">
+
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="max_tau" dimension="per_time" value="0.83 per_time"/>
+        <Constant name="min_tau" dimension="per_time" value="0.093 per_time"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <ConditionalDerivedVariable name="t" dimension="time" exposure="t">
+                <Case condition="(ALPHA + BETA) .eq. 0" value="( 0 ) * TIME_SCALE"/>
+                <Case condition="1/( (ALPHA + BETA) * rateScale )  .lt. ( 0.02 )" value="( (0.02 * rateScale) ) * TIME_SCALE"/>
+                <Case value="( 1/(ALPHA + BETA) ) * TIME_SCALE"/>
+            </ConditionalDerivedVariable>
+
+        </Dynamics>
+
+    </ComponentType>
+
+    <ComponentType name="Ray_nas_tauh"
+                   extends="baseVoltageDepTime"
+                   description="Tau parameter to describe Navp">
+
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+
+        <Requirement name="alpha" dimension="per_time"/>
+        <Requirement name="beta" dimension="per_time"/>
+        <Requirement name="rateScale" dimension="none"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <DerivedVariable name="ALPHA" dimension="none" value="alpha * TIME_SCALE"/>
+            <DerivedVariable name="BETA" dimension="none" value="beta * TIME_SCALE"/>
+
+            <ConditionalDerivedVariable name="t" exposure="t" dimension="time">
+                <Case condition="(ALPHA + BETA) .eq. 0" value="( 0 ) * TIME_SCALE"/>
+                <Case condition="1/( (ALPHA + BETA) * rateScale )  .lt. ( 0.5 )" value="( (0.5 * rateScale) ) * TIME_SCALE"/>
+                <Case value="( 1/(ALPHA + BETA) ) * TIME_SCALE"/>
+            </ConditionalDerivedVariable>
+
+        </Dynamics>
+
+    </ComponentType>
+
+    <ComponentType name="Ray_nas_taus"
+                   extends="baseVoltageDepTime"
+                   description="Tau parameter to describe Navp">
+
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="TEMP_SCALE" dimension="temperature" value="1 K"/>
+        <Constant name="R" dimension="none" value="8.315"/>
+        <Constant name="F" dimension="none" value="96480"/>
+
+        <Requirement name="rateScale" dimension="none"/>
+        <Requirement name="temperature" dimension="temperature"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <DerivedVariable name="T" dimension="none" value="temperature / TEMP_SCALE"/>
+
+            <DerivedVariable name="alpha" dimension="none" value="exp((1e-3*12*(V+45)*F) / (R*(T+0.01)))"/> <!-- NEURON code: 273.16 + celsius-->
+            <DerivedVariable name="beta" dimension="none" value="exp((1e-3*12*0.2*(V+45)*F) / (R*(T+0.01)))"/> <!-- NEURON code: 273.16 + celsius-->
+
+            <DerivedVariable name="tmp" value="beta / (3e-4*(1 + alpha))" dimension="none"/>
+            <ConditionalDerivedVariable name="t" dimension="time" exposure="t" >
+                <Case condition="(tmp / rateScale) .lt. 10" value="10 * rateScale * TIME_SCALE"/>
+                <Case value="tmp * TIME_SCALE"/>
+            </ConditionalDerivedVariable>
+
+        </Dynamics>
+
+    </ComponentType>
+
+    <ComponentType name="Ray_nas_sss_ar2_1"
+                   extends="baseVoltageDepVariable"
+                   description="steadyState parameter to describe Navp">
+
+        <Constant name="no_inact" dimension="none" value="1"/> <!-- 1: no inact, 0: max inact-->
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+
+            <DerivedVariable name="alpha" dimension="none" value="1 / (1 + exp((V+43)/2))"/>
+
+            <DerivedVariable name="x" exposure="x" dimension="none" value="alpha + no_inact*(1 - alpha)"/>
+        </Dynamics>
+
+    </ComponentType>
+
+
+    <ComponentType name="Ray_nas_sss_ar2_0_8"
+                   extends="baseVoltageDepVariable"
+                   description="steadyState parameter to describe Navp">
+
+        <Constant name="no_inact" dimension="none" value="0.8"/> <!-- 1: no inact, 0: max inact-->
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+
+            <DerivedVariable name="alpha" dimension="none" value="1 / (1 + exp((V+43)/2))"/>
+
+            <DerivedVariable name="x" exposure="x" dimension="none" value="alpha + no_inact*(1 - alpha)"/>
+        </Dynamics>
+
+    </ComponentType>
+
+</neuroml>
diff --git a/NeuroML2/channels/pas.channel.nml b/NeuroML2/channels/pas.channel.nml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="pas">
+
+    <notes>NeuroML file containing a single Channel description</notes>
+
+    <ionChannel id="pas" conductance="10pS" type="ionChannelPassive">
+
+        <notes>Simple example of a leak/passive conductance. Note: for GENESIS cells with a single leak conductance,
+        it is better to use the Rm and Em variables for a passive current.</notes>
+
+    </ionChannel>
+
+</neuroml>
diff --git a/NeuroML2/postprocess_cells.py b/NeuroML2/postprocess_cells.py
@@ -0,0 +1,193 @@
+#!/usr/bin/env python3
+"""
+Post process and add biophysics to cells.
+
+We make any updates to the morphology, and add biophysics.
+
+File: NeuroML2/postprocess_cells.py
+
+Copyright 2022 Ankur Sinha
+Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
+"""
+
+
+import random
+
+import neuroml
+from neuroml.loaders import read_neuroml2_file
+from pyneuroml.pynml import write_neuroml2_file
+from neuroml.utils import component_factory
+
+random.seed(1412)
+
+
+def load_and_setup_cell(cellname: str):
+    """Load a cell, and clean it to prepare it for further modifications.
+
+    These operations are common for all cells.
+
+    :param cellname: name of cell.
+        the file containing the cell should then be <cell>.morph.cell.nml
+    :returns: document with cell
+    :rtype: neuroml.NeuroMLDocument
+
+    """
+    celldoc = read_neuroml2_file(
+        f"{cellname}.morph.cell.nml"
+    )  # type: neuroml.NeuroMLDocument
+    cell = celldoc.cells[0]  # type: neuroml.Cell
+    celldoc.networks = []
+    cell.id = cellname
+    cell.notes = cell.notes.replace("GGN_20170309_sc_0_0", cellname)
+    cell.notes += ". Reference: Subhasis Ray, Zane N Aldworth, Mark A Stopfer (2020) Feedback inhibition and its control in an insect olfactory circuit eLife 9:e53281."
+
+    [
+        default_all_group,
+        default_soma_group,
+        default_dendrite_group,
+        default_axon_group,
+    ] = cell.setup_default_segment_groups(
+        use_convention=True,
+        default_groups=["all", "soma_group", "dendrite_group", "axon_group"],
+    )
+
+    # populate default groups
+    for sg in cell.morphology.segment_groups:
+        if "soma" in sg.id and sg.id != "soma_group":
+            default_soma_group.add(neuroml.Include(segment_groups=sg.id))
+        if "axon" in sg.id and sg.id != "axon_group":
+            default_axon_group.add(neuroml.Include(segment_groups=sg.id))
+        if "dend" in sg.id and sg.id != "dendrite_group":
+            default_dendrite_group.add(neuroml.Include(segment_groups=sg.id))
+
+    cell.optimise_segment_groups()
+
+    return celldoc
+
+
+def postprocess_GGN():
+    """Post process GGN and add biophysics."""
+    cellname = "GGN"
+    celldoc = load_and_setup_cell(cellname)
+    cell = celldoc.cells[0]  # type: neuroml.Cell
+
+    # biophysics
+    # all
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="pas",
+        ion_channel="pas",
+        cond_density="0.00003 S_per_cm2",
+        erev="-51 mV",
+        group_id="all",
+        ion="non_specific",
+        ion_chan_def_file="channels/pas.channel.nml",
+    )
+    cell.set_resistivity("0.1 kohm_cm", group_id="all")
+    cell.set_specific_capacitance("1 uF_per_cm2", group_id="all")
+    cell.set_init_memb_potential("-80mV")
+
+    # L1 validation
+    # cell.validate(recursive=True)
+    cell.summary(morph=False, biophys=True)
+    # use pynml writer to also run L2 validation
+    write_neuroml2_file(celldoc, f"{cellname}.cell.nml")
+
+
+def postprocess_KC():
+    """Manually create KC and add biophysics."""
+    celldoc = component_factory("NeuroMLDocument", id="KC_doc")  # type: neuroml.NeuroMLDocument
+    cell = celldoc.add("Cell", id="KC", validate=False)  # type: neuroml.Cell
+    cell.setup_nml_cell()
+    cell.add_segment([0, 0, 0, 20], [0, 0, 6.366, 20], seg_type="soma")
+
+    # biophysics
+    # all
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="pas",
+        ion_channel="pas",
+        cond_density=".0000975 S_per_cm2",
+        erev="-70 mV",
+        group_id="all",
+        ion="non_specific",
+        ion_chan_def_file="channels/pas.channel.nml",
+    )
+    cell.set_resistivity("35.4 ohm_cm", group_id="all")
+    cell.set_specific_capacitance("1 uF_per_cm2", group_id="all")
+    cell.set_init_memb_potential("-80mV")
+
+    # L1 validation
+    # cell.validate(recursive=True)
+    cell.summary(morph=False, biophys=True)
+    # use pynml writer to also run L2 validation
+    write_neuroml2_file(celldoc, "KC.cell.nml")
+
+
+def KC_create_na_channel():
+    """Create the Na channel.
+
+    This will create the Na channel and save it to a file.
+    It will also validate this file.
+
+    returns: name of the created file
+    """
+    na_channel = component_factory(
+        "IonChannelHH",
+        id="na_channel",
+        notes="Sodium channel for HH cell",
+        conductance="10pS",
+        species="na",
+        validate=False,
+    )
+    gate_m = component_factory(
+        "GateHHRates",
+        id="m",
+        instances="3",
+        notes="m gate for na channel",
+        validate=False,
+    )
+    m_forward_rate = component_factory(
+        "HHRate", type="HHExpLinearRate", rate="1per_ms", midpoint="-40mV", scale="10mV"
+    )
+    m_reverse_rate = component_factory(
+        "HHRate", type="HHExpRate", rate="4per_ms", midpoint="-65mV", scale="-18mV"
+    )
+
+    gate_m.add(m_forward_rate, hint="forward_rate", validate=False)
+    gate_m.add(m_reverse_rate, hint="reverse_rate")
+    na_channel.add(gate_m)
+
+    gate_h = component_factory(
+        "GateHHRates",
+        id="h",
+        instances="1",
+        notes="h gate for na channel",
+        validate=False,
+    )
+    h_forward_rate = component_factory(
+        "HHRate", type="HHExpRate", rate="0.07per_ms", midpoint="-65mV", scale="-20mV"
+    )
+    h_reverse_rate = component_factory(
+        "HHRate", type="HHSigmoidRate", rate="1per_ms", midpoint="-35mV", scale="10mV"
+    )
+    gate_h.add(h_forward_rate, hint="forward_rate", validate=False)
+    gate_h.add(h_reverse_rate, hint="reverse_rate")
+    na_channel.add(gate_h)
+
+    na_channel_doc = component_factory(
+        "NeuroMLDocument", id="na_channel", notes="Na channel for HH neuron"
+    )
+    na_channel_fn = "HH_example_na_channel.nml"
+    na_channel_doc.add(na_channel)
+    na_channel_doc.validate(recursive=True)
+
+    write_neuroml2_file(
+        nml2_doc=na_channel_doc, nml2_file_name=na_channel_fn, validate=True
+    )
+
+    return na_channel_fn
+
+
+if __name__ == "__main__":
+    postprocess_GGN()