From 29199e0708dc04e09dcb2edea38662b76f6e4677 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Wed, 19 Jun 2024 11:07:28 +0100
Subject: [PATCH] Add examples with tests for various ways to include
 <morphology> and <biophysicalProperties> in <cell>

---
 .gitignore                                    |  12 +
 LEMSexamples/morphologies/.test.jnml.omt      |  17 ++
 .../morphologies/.test.jnmleden.multi.omt     |  20 ++
 .../morphologies/.test.jnmleden.multi.out.omt |  20 ++
 LEMSexamples/morphologies/.test.jnmleden.omt  |  17 ++
 .../morphologies/.test.jnmleden.out.omt       |  17 ++
 .../morphologies/.test.jnmlnetpyne.multi.omt  |  20 ++
 .../.test.jnmlnetpyne.multi.out.omt           |  20 ++
 .../morphologies/.test.jnmlnetpyne.omt        |  20 ++
 .../morphologies/.test.jnmlnetpyne.out.omt    |  20 ++
 .../morphologies/.test.jnmlnrn.multi.omt      |  20 ++
 .../morphologies/.test.jnmlnrn.multi.out.omt  |  20 ++
 LEMSexamples/morphologies/.test.jnmlnrn.omt   |  20 ++
 .../morphologies/.test.jnmlnrn.out.omt        |  20 ++
 LEMSexamples/morphologies/.test.mep           |   6 +
 LEMSexamples/morphologies/.test.multi.mep     |   6 +
 LEMSexamples/morphologies/.test.validate.omt  |   5 +
 LEMSexamples/morphologies/Ca_conc.nml         |   8 +
 LEMSexamples/morphologies/Ca_pyr.channel.nml  | 106 ++++++++
 .../morphologies/Kahp_pyr.channel.nml         | 106 ++++++++
 LEMSexamples/morphologies/Kdr_pyr.channel.nml |  60 +++++
 LEMSexamples/morphologies/LEMS_m_in_b_in.xml  |  67 +++++
 LEMSexamples/morphologies/LEMS_m_in_b_out.xml |  66 +++++
 LEMSexamples/morphologies/LEMS_m_out_b_in.xml |  66 +++++
 .../morphologies/LEMS_m_out_b_out.xml         |  45 ++++
 LEMSexamples/morphologies/LEMS_pyrfull_in.xml |  92 +++++++
 .../morphologies/LEMS_pyrfull_out.xml         |  91 +++++++
 .../LeakConductance_pyr.channel.nml           |  13 +
 LEMSexamples/morphologies/Na_pyr.channel.nml  |  68 +++++
 LEMSexamples/morphologies/README.md           |  47 ++++
 .../morphologies/network_m_out_b_out.net.nml  |  29 +++
 LEMSexamples/morphologies/pyr_4_sym.cell.nml  | 246 ++++++++++++++++++
 .../morphologies/pyr_4_sym_soma_morph.nml     |  33 +++
 LEMSexamples/morphologies/pyr_biophysics.nml  |  50 ++++
 .../morphologies/pyr_full_morph_biophys.nml   | 241 +++++++++++++++++
 .../morphologies/pyr_full_out.cell.nml        |  13 +
 .../morphologies/pyr_morphology.cell.nml      | 201 ++++++++++++++
 .../morphologies/pyr_soma_m_in_b_in.cell.nml  |  84 ++++++
 .../morphologies/pyr_soma_m_in_b_out.cell.nml |  39 +++
 .../morphologies/pyr_soma_m_out_b_in.cell.nml |  60 +++++
 .../pyr_soma_m_out_b_out.cell.nml             |  13 +
 LEMSexamples/morphologies/pyrfull_in.net.nml  |  26 ++
 LEMSexamples/morphologies/pyrfull_out.net.nml |  26 ++
 LEMSexamples/morphologies/test_all.sh         |  29 +++
 44 files changed, 2205 insertions(+)
 create mode 100644 LEMSexamples/morphologies/.test.jnml.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmleden.multi.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmleden.multi.out.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmleden.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmleden.out.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmlnetpyne.multi.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmlnetpyne.multi.out.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmlnetpyne.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmlnetpyne.out.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmlnrn.multi.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmlnrn.multi.out.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmlnrn.omt
 create mode 100644 LEMSexamples/morphologies/.test.jnmlnrn.out.omt
 create mode 100644 LEMSexamples/morphologies/.test.mep
 create mode 100644 LEMSexamples/morphologies/.test.multi.mep
 create mode 100644 LEMSexamples/morphologies/.test.validate.omt
 create mode 100644 LEMSexamples/morphologies/Ca_conc.nml
 create mode 100644 LEMSexamples/morphologies/Ca_pyr.channel.nml
 create mode 100644 LEMSexamples/morphologies/Kahp_pyr.channel.nml
 create mode 100644 LEMSexamples/morphologies/Kdr_pyr.channel.nml
 create mode 100644 LEMSexamples/morphologies/LEMS_m_in_b_in.xml
 create mode 100644 LEMSexamples/morphologies/LEMS_m_in_b_out.xml
 create mode 100644 LEMSexamples/morphologies/LEMS_m_out_b_in.xml
 create mode 100644 LEMSexamples/morphologies/LEMS_m_out_b_out.xml
 create mode 100644 LEMSexamples/morphologies/LEMS_pyrfull_in.xml
 create mode 100644 LEMSexamples/morphologies/LEMS_pyrfull_out.xml
 create mode 100644 LEMSexamples/morphologies/LeakConductance_pyr.channel.nml
 create mode 100644 LEMSexamples/morphologies/Na_pyr.channel.nml
 create mode 100644 LEMSexamples/morphologies/README.md
 create mode 100644 LEMSexamples/morphologies/network_m_out_b_out.net.nml
 create mode 100644 LEMSexamples/morphologies/pyr_4_sym.cell.nml
 create mode 100644 LEMSexamples/morphologies/pyr_4_sym_soma_morph.nml
 create mode 100644 LEMSexamples/morphologies/pyr_biophysics.nml
 create mode 100644 LEMSexamples/morphologies/pyr_full_morph_biophys.nml
 create mode 100644 LEMSexamples/morphologies/pyr_full_out.cell.nml
 create mode 100644 LEMSexamples/morphologies/pyr_morphology.cell.nml
 create mode 100644 LEMSexamples/morphologies/pyr_soma_m_in_b_in.cell.nml
 create mode 100644 LEMSexamples/morphologies/pyr_soma_m_in_b_out.cell.nml
 create mode 100644 LEMSexamples/morphologies/pyr_soma_m_out_b_in.cell.nml
 create mode 100644 LEMSexamples/morphologies/pyr_soma_m_out_b_out.cell.nml
 create mode 100644 LEMSexamples/morphologies/pyrfull_in.net.nml
 create mode 100644 LEMSexamples/morphologies/pyrfull_out.net.nml
 create mode 100755 LEMSexamples/morphologies/test_all.sh

diff --git a/.gitignore b/.gitignore
index e58f53e..0dfe0af 100644
--- a/.gitignore
+++ b/.gitignore
@@ -68,3 +68,15 @@ examples/*.pov
 /LEMSexamples/tmp
 arm64
 /examples/NML2_SingleCompHHCell.nml__flattened.xml
+/LEMSexamples/morphologies/*.mod
+/LEMSexamples/morphologies/*.c
+/LEMSexamples/morphologies/*.so
+*eden.py
+*netpyne.py
+*nrn.py
+/LEMSexamples/morphologies/*.dat
+/LEMSexamples/morphologies/*.hoc
+/LEMSexamples/morphologies/NET_m_in_b_in.net.nml
+/LEMSexamples/morphologies/simulator.props
+/LEMSexamples/morphologies/NET_m_in_b_out.net.nml
+/LEMSexamples/morphologies/NET_m_out_b_in.net.nml
diff --git a/LEMSexamples/morphologies/.test.jnml.omt b/LEMSexamples/morphologies/.test.jnml.omt
new file mode 100644
index 0000000..15552fa
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnml.omt
@@ -0,0 +1,17 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.004018425953151025
diff --git a/LEMSexamples/morphologies/.test.jnmleden.multi.omt b/LEMSexamples/morphologies/.test.jnmleden.multi.omt
new file mode 100644
index 0000000..584aad5
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmleden.multi.omt
@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_in.xml
+engine: jNeuroML_EDEN
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.017719626168224333
+
+
+        
diff --git a/LEMSexamples/morphologies/.test.jnmleden.multi.out.omt b/LEMSexamples/morphologies/.test.jnmleden.multi.out.omt
new file mode 100644
index 0000000..b81acec
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmleden.multi.out.omt
@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_out.xml
+engine: jNeuroML_EDEN
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.017719626168224333
+
+
+        
diff --git a/LEMSexamples/morphologies/.test.jnmleden.omt b/LEMSexamples/morphologies/.test.jnmleden.omt
new file mode 100644
index 0000000..b488705
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmleden.omt
@@ -0,0 +1,17 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML_EDEN
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.0024858998690222445
diff --git a/LEMSexamples/morphologies/.test.jnmleden.out.omt b/LEMSexamples/morphologies/.test.jnmleden.out.omt
new file mode 100644
index 0000000..e3a1926
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmleden.out.omt
@@ -0,0 +1,17 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_out_b_out.xml
+engine: jNeuroML_EDEN
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0.0024858998690222445
diff --git a/LEMSexamples/morphologies/.test.jnmlnetpyne.multi.omt b/LEMSexamples/morphologies/.test.jnmlnetpyne.multi.omt
new file mode 100644
index 0000000..51aefcc
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmlnetpyne.multi.omt
@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_in.xml
+engine: jNeuroML_NetPyNE
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+        
diff --git a/LEMSexamples/morphologies/.test.jnmlnetpyne.multi.out.omt b/LEMSexamples/morphologies/.test.jnmlnetpyne.multi.out.omt
new file mode 100644
index 0000000..aa53dcc
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmlnetpyne.multi.out.omt
@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_out.xml
+engine: jNeuroML_NetPyNE
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+        
diff --git a/LEMSexamples/morphologies/.test.jnmlnetpyne.omt b/LEMSexamples/morphologies/.test.jnmlnetpyne.omt
new file mode 100644
index 0000000..f43719a
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmlnetpyne.omt
@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML_NetPyNE
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+        
diff --git a/LEMSexamples/morphologies/.test.jnmlnetpyne.out.omt b/LEMSexamples/morphologies/.test.jnmlnetpyne.out.omt
new file mode 100644
index 0000000..4f3a609
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmlnetpyne.out.omt
@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_out_b_out.xml
+engine: jNeuroML_NetPyNE
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+        
diff --git a/LEMSexamples/morphologies/.test.jnmlnrn.multi.omt b/LEMSexamples/morphologies/.test.jnmlnrn.multi.omt
new file mode 100644
index 0000000..6df86c8
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmlnrn.multi.omt
@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_in.xml
+engine: jNeuroML_NEURON
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+        
diff --git a/LEMSexamples/morphologies/.test.jnmlnrn.multi.out.omt b/LEMSexamples/morphologies/.test.jnmlnrn.multi.out.omt
new file mode 100644
index 0000000..356c609
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmlnrn.multi.out.omt
@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_pyrfull_out.xml
+engine: jNeuroML_NEURON
+mep: .test.multi.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidals_0.0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+        
diff --git a/LEMSexamples/morphologies/.test.jnmlnrn.omt b/LEMSexamples/morphologies/.test.jnmlnrn.omt
new file mode 100644
index 0000000..191f96e
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmlnrn.omt
@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_in_b_in.xml
+engine: jNeuroML_NEURON
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+        
diff --git a/LEMSexamples/morphologies/.test.jnmlnrn.out.omt b/LEMSexamples/morphologies/.test.jnmlnrn.out.omt
new file mode 100644
index 0000000..4d47a59
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.jnmlnrn.out.omt
@@ -0,0 +1,20 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_m_out_b_out.xml
+engine: jNeuroML_NEURON
+mep: .test.mep
+experiments:
+  Current clamp pyramidal:
+    observables:
+      spike times:
+        file:
+          path: pyramidal_soma_0.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection:
+          method: threshold
+          threshold: 0
+        tolerance: 0
+
+
+        
diff --git a/LEMSexamples/morphologies/.test.mep b/LEMSexamples/morphologies/.test.mep
new file mode 100644
index 0000000..88d6fa5
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.mep
@@ -0,0 +1,6 @@
+system: Testing a single compartment cell
+
+experiments:
+  Current clamp pyramidal:
+    expected:
+        spike times: [102.49, 120.78, 148.66, 256.3125, 330.84000000000003, 408.0575, 484.6375, 561.1650000000001]
diff --git a/LEMSexamples/morphologies/.test.multi.mep b/LEMSexamples/morphologies/.test.multi.mep
new file mode 100644
index 0000000..741189f
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.multi.mep
@@ -0,0 +1,6 @@
+system: Testing a cell
+
+experiments:
+  Current clamp pyramidal:
+    expected:
+        spike times: [134.24, 401.25]
diff --git a/LEMSexamples/morphologies/.test.validate.omt b/LEMSexamples/morphologies/.test.validate.omt
new file mode 100644
index 0000000..7402c51
--- /dev/null
+++ b/LEMSexamples/morphologies/.test.validate.omt
@@ -0,0 +1,5 @@
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+# This test will validate all of the NeuroML 2 files in the current directory using: jnml -validate *.nml
+target: "*cell.nml *channel.nml C*.nml"
+engine: jNeuroML_validate
diff --git a/LEMSexamples/morphologies/Ca_conc.nml b/LEMSexamples/morphologies/Ca_conc.nml
new file mode 100644
index 0000000..985481f
--- /dev/null
+++ b/LEMSexamples/morphologies/Ca_conc.nml
@@ -0,0 +1,8 @@
+<?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="Ca_conc">
+        
+    <notes>NeuroML file describing intracellular Calcium dynamics, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+        
+    <fixedFactorConcentrationModel id="Ca_conc" restingConc="0.0mM" decayConstant="0.1s" ion="ca" rho="9543.150099999999mol_per_m_per_A_per_s"/>
+    
+</neuroml>
diff --git a/LEMSexamples/morphologies/Ca_pyr.channel.nml b/LEMSexamples/morphologies/Ca_pyr.channel.nml
new file mode 100644
index 0000000..d878a9d
--- /dev/null
+++ b/LEMSexamples/morphologies/Ca_pyr.channel.nml
@@ -0,0 +1,106 @@
+<?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="Ca_pyr">
+        
+    <notes>NeuroML file containing a single Calcium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+        
+    <ionChannel id="Ca_pyr" conductance="10pS" type="ionChannelHH" species="ca">
+                
+        <notes>NeuroML file containing a single Calcium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+                        
+        
+        <annotation>
+                        
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                                
+                <rdf:Description rdf:about="Ca_pyr">
+                                        
+                    
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                                                
+                        <rdf:Bag>
+                                                        
+                            <rdf:li>Traub, R. D., Wong, R. K., Miles, R., and Michelson, H. (1991). A model of a CA3 hippocampal pyramidal neuron incorporating voltage-clamp data on intrinsic conductances. Journal of neurophysiology, 66(2), 635-50.</rdf:li>
+                                                        
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/1663538"/>
+                                                    
+                        </rdf:Bag>
+                                            
+                    </bqmodel:isDescribedBy>
+                                    
+                    
+                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                                                
+                        <rdf:Bag>
+                                                        
+                            <rdf:li>Ca channels</rdf:li>
+                                                        
+                            <rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/NeuronProp.aspx?id=259&amp;mo=1&amp;re=&amp;pr=C"/>
+                                                    
+                        </rdf:Bag>
+                                            
+                    </bqbiol:isVersionOf>
+                                    
+                </rdf:Description>
+                            
+            </rdf:RDF>
+                    
+        </annotation>
+                
+        <gate id="m" type="gateHHrates" instances="2">
+                        
+            <forwardRate type="HHSigmoidRate" rate="1.6e3per_s" scale="0.01389V" midpoint="5e-03V"/>
+                        
+            <reverseRate type="HHExpLinearRate" rate="1e2per_s" scale="-0.005V" midpoint="-8.9e-3V"/>
+                    
+        </gate>
+                
+        <gate id="h" type="gateHHtauInf" instances="1">
+                        
+            <timeCourse type="Ca_pyr_h_tau_tau"/>
+                        
+            <steadyState type="Ca_pyr_h_inf_inf"/>
+                    
+        </gate>
+                                    
+    
+    </ionChannel>
+        
+    <ComponentType name="Ca_pyr_h_tau_tau" extends="baseVoltageDepTime">
+                
+        <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
+                
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 V"/>
+                
+        <Dynamics>
+                        
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+                        
+            <DerivedVariable name="t" exposure="t" dimension="time" value="(0.2) * TIME_SCALE"/>
+                    
+        </Dynamics>
+            
+    </ComponentType>
+        
+    <ComponentType name="Ca_pyr_h_inf_inf" extends="baseVoltageDepVariable">
+                
+        <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
+                
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 V"/>
+                
+        <Dynamics>
+                        
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+                        
+            <ConditionalDerivedVariable name="x" exposure="x" dimension="none">
+                                
+                <Case condition="V  .gt. ( -0.06 )" value=" (exp (-50*(V + 0.06))) "/>
+                                
+                <Case value=" 1"/>
+                            
+            </ConditionalDerivedVariable>
+                    
+        </Dynamics>
+            
+    </ComponentType>
+    
+</neuroml>
diff --git a/LEMSexamples/morphologies/Kahp_pyr.channel.nml b/LEMSexamples/morphologies/Kahp_pyr.channel.nml
new file mode 100644
index 0000000..b3cfbaa
--- /dev/null
+++ b/LEMSexamples/morphologies/Kahp_pyr.channel.nml
@@ -0,0 +1,106 @@
+<?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="Kahp_pyr">
+        
+    <notes>NeuroML file containing a single Calcium-dependent Potassium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+        
+    <ionChannel id="Kahp_pyr" conductance="10pS" type="ionChannelHH" species="k">
+                
+        <notes>NeuroML file containing a single Calcium-dependent Potassium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+                        
+        
+        <annotation>
+                        
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                                
+                <rdf:Description rdf:about="Kahp_pyr">
+                                        
+                    
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                                                
+                        <rdf:Bag>
+                                                        
+                            <rdf:li>Traub, R. D., Wong, R. K., Miles, R., and Michelson, H. (1991). A model of a CA3 hippocampal pyramidal neuron incorporating voltage-clamp data on intrinsic conductances. Journal of neurophysiology, 66(2), 635-50.</rdf:li>
+                                                        
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/1663538"/>
+                                                    
+                        </rdf:Bag>
+                                            
+                    </bqmodel:isDescribedBy>
+                                    
+                    
+                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                                                
+                        <rdf:Bag>
+                                                        
+                            <rdf:li>K channels</rdf:li>
+                                                        
+                            <rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/NeuronProp.aspx?id=259&amp;mo=1&amp;re=&amp;pr=C"/>
+                                                    
+                        </rdf:Bag>
+                                            
+                    </bqbiol:isVersionOf>
+                                    
+                </rdf:Description>
+                            
+            </rdf:RDF>
+                    
+        </annotation>
+                
+        <gate id="z" type="gateHHrates" instances="1">
+                        
+            <forwardRate type="Kahp_pyr_z_alpha_rate"/>
+                        
+            <reverseRate type="Kahp_pyr_z_beta_rate"/>
+                    
+        </gate>
+                                    
+    
+    </ionChannel>
+        
+    <ComponentType name="Kahp_pyr_z_alpha_rate" extends="baseVoltageConcDepRate">
+                
+        <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
+                
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 V"/>
+                
+        <Constant name="CONC_SCALE" dimension="concentration" value="1 mM"/>
+                
+        <Dynamics>
+                        
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+                        
+            <DerivedVariable name="ca_conc" dimension="none" value="caConc / CONC_SCALE"/>
+                        
+            <ConditionalDerivedVariable name="r" exposure="r" dimension="per_time">
+                                
+                <Case condition="ca_conc  .lt. ( 500.0 )" value="( 0.4 * ca_conc ) / TIME_SCALE"/>
+                                
+                <Case value="( 200) / TIME_SCALE"/>
+                            
+            </ConditionalDerivedVariable>
+                    
+        </Dynamics>
+            
+    </ComponentType>
+        
+    <ComponentType name="Kahp_pyr_z_beta_rate" extends="baseVoltageConcDepRate">
+                
+        <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
+                
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 V"/>
+                
+        <Constant name="CONC_SCALE" dimension="concentration" value="1 mM"/>
+                
+        <Dynamics>
+                        
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+                        
+            <DerivedVariable name="ca_conc" dimension="none" value="caConc / CONC_SCALE"/>
+                        
+            <DerivedVariable name="r" exposure="r" dimension="per_time" value="(20) / TIME_SCALE"/>
+                    
+        </Dynamics>
+            
+    </ComponentType>
+    
+</neuroml>
diff --git a/LEMSexamples/morphologies/Kdr_pyr.channel.nml b/LEMSexamples/morphologies/Kdr_pyr.channel.nml
new file mode 100644
index 0000000..20364ae
--- /dev/null
+++ b/LEMSexamples/morphologies/Kdr_pyr.channel.nml
@@ -0,0 +1,60 @@
+<?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="Kdr_pyr">
+        
+    <notes>NeuroML file containing a single Potassium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+        
+    <ionChannel id="Kdr_pyr" conductance="10pS" type="ionChannelHH" species="k">
+                
+        <notes>NeuroML file containing a single Potassium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+                        
+        
+        <annotation>
+                        
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                                
+                <rdf:Description rdf:about="Kdr_pyr">
+                                        
+                    
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                                                
+                        <rdf:Bag>
+                                                        
+                            <rdf:li>Traub, R. D., Wong, R. K., Miles, R., and Michelson, H. (1991). A model of a CA3 hippocampal pyramidal neuron incorporating voltage-clamp data on intrinsic conductances. Journal of neurophysiology, 66(2), 635-50.</rdf:li>
+                                                        
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/1663538"/>
+                                                    
+                        </rdf:Bag>
+                                            
+                    </bqmodel:isDescribedBy>
+                                    
+                    
+                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                                                
+                        <rdf:Bag>
+                                                        
+                            <rdf:li>K channels</rdf:li>
+                                                        
+                            <rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/NeuronProp.aspx?id=259&amp;mo=1&amp;re=&amp;pr=C"/>
+                                                    
+                        </rdf:Bag>
+                                            
+                    </bqbiol:isVersionOf>
+                                    
+                </rdf:Description>
+                            
+            </rdf:RDF>
+                    
+        </annotation>
+                
+        <gate id="n" type="gateHHrates" instances="1">
+                        
+            <forwardRate type="HHExpLinearRate" rate="40per_s" scale="0.005V" midpoint="-2.49e-2V"/>
+                        
+            <reverseRate type="HHExpRate" rate="125per_s" scale="-0.04V" midpoint="-4e-2V"/>
+                    
+        </gate>
+                                    
+    
+    </ionChannel>
+    
+</neuroml>
diff --git a/LEMSexamples/morphologies/LEMS_m_in_b_in.xml b/LEMSexamples/morphologies/LEMS_m_in_b_in.xml
new file mode 100644
index 0000000..993aed2
--- /dev/null
+++ b/LEMSexamples/morphologies/LEMS_m_in_b_in.xml
@@ -0,0 +1,67 @@
+<Lems xmlns="http://www.neuroml.org/lems/0.7.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/lems/0.7.2  https://raw.github.com/LEMS/LEMS/development/Schemas/LEMS/LEMS_v0.7.2.xsd">
+
+    <Target component="sim1" reportFile="simulator.props" timesFile="time.dat"/>
+
+        <!--Include standard NeuroML 2 ComponentType definitions-->
+
+    <Include file="Cells.xml"/>
+    <Include file="Networks.xml"/>
+    <Include file="Simulation.xml"/>
+
+    <Include file="Ca_pyr.channel.nml"/>
+    <Include file="Ca_conc.nml"/>
+    <Include file="Kahp_pyr.channel.nml"/>
+    <Include file="Kdr_pyr.channel.nml"/>
+    <Include file="LeakConductance_pyr.channel.nml"/>
+    <Include file="Na_pyr.channel.nml"/>
+
+    
+        <!--   Cell files-->
+    <Include file="pyr_soma_m_in_b_in.cell.nml"/>
+
+    <pulseGenerator id="Input_3" delay="100.0ms" duration="500.0ms" amplitude="2.0E-4uA"/>
+
+    <network id="network" type="networkWithTemperature" temperature="6.3 degC">
+
+        <population id="pyramidal_soma" component="pyr_soma_m_in_b_in" type="populationList" size="1">
+           <annotation>
+                <property tag="color" value="0.7421875 0.07421875 0.95703125"/>
+            </annotation>
+            <instance id="0">
+                <location x="400.0" y="0.0" z="0.0"/>
+            </instance>
+        </population>
+
+        <inputList id="Input_3" component="Input_3" population="pyramidal_soma">
+            <input id="0" target="../pyramidal_soma/0/pyr_soma_m_in_b_in" destination="synapses"/>
+        </inputList>
+
+
+    </network>
+    
+
+        <!--Note: this could be: Simulation id="sim1" ... , but Component type="Simulation" ... 
+        is used to allow validation of this file according to the LEMS schema specified above...-->
+    <Component type="Simulation" id="sim1" length="700.0ms" step="0.0025ms" target="network">
+        
+    
+        <Display id="pyramidal_soma_v" title="ACnet2: TestSoma, pyramidal_soma, VOLTAGE" xmin="-70.0" xmax="770.0" ymin="-104.0" ymax="64.0" timeScale="1ms">
+            <Line id="VOLTAGE-pyramidal_soma_0" timeScale="1ms" quantity="pyramidal_soma/0/pyr_soma_m_in_b_in/v" scale="1 mV" color="#000000"/>
+        </Display>
+    
+        <Display id="GraphWin_12" title="ACnet2: TestSoma, pyramidal_soma, Ca_conc:CONC:ca" xmin="-70.0" xmax="770.0" ymin="-1E-5" ymax="9E-5" timeScale="1ms">
+            <Line id="Ca_conc_CONC_ca-pyramidal_soma_0" timeScale="1ms" quantity="pyramidal_soma/0/pyr_soma_m_in_b_in/caConc" scale="1 mol_per_cm3" color="#000000"/>
+        </Display>
+    
+    
+        <OutputFile id="pyramidal_soma_v_OF" fileName="pyramidal_soma_0.dat">
+            <OutputColumn id="v" quantity="pyramidal_soma/0/pyr_soma_m_in_b_in/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_ca_2_OF" fileName="pyramidal_soma_0.Ca_conc_CONC_ca.dat">
+            <OutputColumn id="caConc" quantity="pyramidal_soma/0/pyr_soma_m_in_b_in/caConc"/>
+        </OutputFile>
+    </Component>
+
+
+</Lems>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/LEMS_m_in_b_out.xml b/LEMSexamples/morphologies/LEMS_m_in_b_out.xml
new file mode 100644
index 0000000..f1f325f
--- /dev/null
+++ b/LEMSexamples/morphologies/LEMS_m_in_b_out.xml
@@ -0,0 +1,66 @@
+<Lems xmlns="http://www.neuroml.org/lems/0.7.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/lems/0.7.2  https://raw.github.com/LEMS/LEMS/development/Schemas/LEMS/LEMS_v0.7.2.xsd">
+
+    <Target component="sim1" reportFile="simulator.props" timesFile="time.dat"/>
+
+        <!--Include standard NeuroML 2 ComponentType definitions-->
+
+    <Include file="Cells.xml"/>
+    <Include file="Networks.xml"/>
+    <Include file="Simulation.xml"/>
+
+    <Include file="Ca_pyr.channel.nml"/>
+    <Include file="Ca_conc.nml"/>
+    <Include file="Kahp_pyr.channel.nml"/>
+    <Include file="Kdr_pyr.channel.nml"/>
+    <Include file="LeakConductance_pyr.channel.nml"/>
+    <Include file="Na_pyr.channel.nml"/>
+    
+        <!--   Cell files-->
+    <Include file="pyr_soma_m_in_b_out.cell.nml"/>
+
+    <pulseGenerator id="Input_3" delay="100.0ms" duration="500.0ms" amplitude="2.0E-4uA"/>
+
+    <network id="network" type="networkWithTemperature" temperature="6.3 degC">
+
+        <population id="pyramidal_soma" component="pyr_soma_m_in_b_out" type="populationList" size="1">
+           <annotation>
+                <property tag="color" value="0.7421875 0.07421875 0.95703125"/>
+            </annotation>
+            <instance id="0">
+                <location x="400.0" y="0.0" z="0.0"/>
+            </instance>
+        </population>
+
+        <inputList id="Input_3" component="Input_3" population="pyramidal_soma">
+            <input id="0" target="../pyramidal_soma/0/pyr_soma_m_out_b_in" destination="synapses"/>
+        </inputList>
+
+
+    </network>
+    
+
+        <!--Note: this could be: Simulation id="sim1" ... , but Component type="Simulation" ... 
+        is used to allow validation of this file according to the LEMS schema specified above...-->
+    <Component type="Simulation" id="sim1" length="700.0ms" step="0.0025ms" target="network">
+        
+    
+        <Display id="pyramidal_soma_v" title="ACnet2: TestSoma, pyramidal_soma, VOLTAGE" xmin="-70.0" xmax="770.0" ymin="-104.0" ymax="64.0" timeScale="1ms">
+            <Line id="VOLTAGE-pyramidal_soma_0" timeScale="1ms" quantity="pyramidal_soma/0/pyr_soma_m_in_b_out/v" scale="1 mV" color="#000000"/>
+        </Display>
+    
+        <Display id="GraphWin_12" title="ACnet2: TestSoma, pyramidal_soma, Ca_conc:CONC:ca" xmin="-70.0" xmax="770.0" ymin="-1E-5" ymax="9E-5" timeScale="1ms">
+            <Line id="Ca_conc_CONC_ca-pyramidal_soma_0" timeScale="1ms" quantity="pyramidal_soma/0/pyr_soma_m_in_b_out/caConc" scale="1 mol_per_cm3" color="#000000"/>
+        </Display>
+    
+    
+        <OutputFile id="pyramidal_soma_v_OF" fileName="pyramidal_soma_0.dat">
+            <OutputColumn id="v" quantity="pyramidal_soma/0/pyr_soma_m_in_b_out/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_ca_2_OF" fileName="pyramidal_soma_0.Ca_conc_CONC_ca.dat">
+            <OutputColumn id="caConc" quantity="pyramidal_soma/0/pyr_soma_m_in_b_out/caConc"/>
+        </OutputFile>
+    </Component>
+
+
+</Lems>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/LEMS_m_out_b_in.xml b/LEMSexamples/morphologies/LEMS_m_out_b_in.xml
new file mode 100644
index 0000000..dfb2434
--- /dev/null
+++ b/LEMSexamples/morphologies/LEMS_m_out_b_in.xml
@@ -0,0 +1,66 @@
+<Lems xmlns="http://www.neuroml.org/lems/0.7.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/lems/0.7.2  https://raw.github.com/LEMS/LEMS/development/Schemas/LEMS/LEMS_v0.7.2.xsd">
+
+    <Target component="sim1" reportFile="simulator.props" timesFile="time.dat"/>
+
+        <!--Include standard NeuroML 2 ComponentType definitions-->
+
+    <Include file="Cells.xml"/>
+    <Include file="Networks.xml"/>
+    <Include file="Simulation.xml"/>
+
+    <Include file="Ca_pyr.channel.nml"/>
+    <Include file="Ca_conc.nml"/>
+    <Include file="Kahp_pyr.channel.nml"/>
+    <Include file="Kdr_pyr.channel.nml"/>
+    <Include file="LeakConductance_pyr.channel.nml"/>
+    <Include file="Na_pyr.channel.nml"/>
+    
+        <!--   Cell files-->
+    <Include file="pyr_soma_m_out_b_in.cell.nml"/>
+
+    <pulseGenerator id="Input_3" delay="100.0ms" duration="500.0ms" amplitude="2.0E-4uA"/>
+
+    <network id="network" type="networkWithTemperature" temperature="6.3 degC">
+
+        <population id="pyramidal_soma" component="pyr_soma_m_out_b_in" type="populationList" size="1">
+           <annotation>
+                <property tag="color" value="0.7421875 0.07421875 0.95703125"/>
+            </annotation>
+            <instance id="0">
+                <location x="400.0" y="0.0" z="0.0"/>
+            </instance>
+        </population>
+
+        <inputList id="Input_3" component="Input_3" population="pyramidal_soma">
+            <input id="0" target="../pyramidal_soma/0/pyr_soma_m_out_b_in" destination="synapses"/>
+        </inputList>
+
+
+    </network>
+    
+
+        <!--Note: this could be: Simulation id="sim1" ... , but Component type="Simulation" ... 
+        is used to allow validation of this file according to the LEMS schema specified above...-->
+    <Component type="Simulation" id="sim1" length="700.0ms" step="0.0025ms" target="network">
+        
+    
+        <Display id="pyramidal_soma_v" title="ACnet2: TestSoma, pyramidal_soma, VOLTAGE" xmin="-70.0" xmax="770.0" ymin="-104.0" ymax="64.0" timeScale="1ms">
+            <Line id="VOLTAGE-pyramidal_soma_0" timeScale="1ms" quantity="pyramidal_soma/0/pyr_soma_m_out_b_in/v" scale="1 mV" color="#000000"/>
+        </Display>
+    
+        <Display id="GraphWin_12" title="ACnet2: TestSoma, pyramidal_soma, Ca_conc:CONC:ca" xmin="-70.0" xmax="770.0" ymin="-1E-5" ymax="9E-5" timeScale="1ms">
+            <Line id="Ca_conc_CONC_ca-pyramidal_soma_0" timeScale="1ms" quantity="pyramidal_soma/0/pyr_soma_m_out_b_in/caConc" scale="1 mol_per_cm3" color="#000000"/>
+        </Display>
+    
+    
+        <OutputFile id="pyramidal_soma_v_OF" fileName="pyramidal_soma_0.dat">
+            <OutputColumn id="v" quantity="pyramidal_soma/0/pyr_soma_m_out_b_in/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_ca_2_OF" fileName="pyramidal_soma_0.Ca_conc_CONC_ca.dat">
+            <OutputColumn id="caConc" quantity="pyramidal_soma/0/pyr_soma_m_out_b_in/caConc"/>
+        </OutputFile>
+    </Component>
+
+
+</Lems>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/LEMS_m_out_b_out.xml b/LEMSexamples/morphologies/LEMS_m_out_b_out.xml
new file mode 100644
index 0000000..8055450
--- /dev/null
+++ b/LEMSexamples/morphologies/LEMS_m_out_b_out.xml
@@ -0,0 +1,45 @@
+<Lems xmlns="http://www.neuroml.org/lems/0.7.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/lems/0.7.2  https://raw.github.com/LEMS/LEMS/development/Schemas/LEMS/LEMS_v0.7.2.xsd">
+
+    <Target component="sim1" reportFile="simulator.props" timesFile="time.dat"/>
+
+        <!--Include standard NeuroML 2 ComponentType definitions-->
+
+    <Include file="Cells.xml"/>
+    <Include file="Networks.xml"/>
+    <Include file="Simulation.xml"/>
+
+    <Include file="Ca_pyr.channel.nml"/>
+    <Include file="Ca_conc.nml"/>
+    <Include file="Kahp_pyr.channel.nml"/>
+    <Include file="Kdr_pyr.channel.nml"/>
+    <Include file="LeakConductance_pyr.channel.nml"/>
+    <Include file="Na_pyr.channel.nml"/>
+    
+        <!--   Network files-->
+    <Include file="network_m_out_b_out.net.nml"/>
+    
+        <!--Note: this could be: Simulation id="sim1" ... , but Component type="Simulation" ... 
+        is used to allow validation of this file according to the LEMS schema specified above...-->
+    <Component type="Simulation" id="sim1" length="700.0ms" step="0.0025ms" target="network">
+        
+    
+        <Display id="pyramidal_soma_v" title="ACnet2: TestSoma, pyramidal_soma, VOLTAGE" xmin="-70.0" xmax="770.0" ymin="-104.0" ymax="64.0" timeScale="1ms">
+            <Line id="VOLTAGE-pyramidal_soma_0" timeScale="1ms" quantity="pyramidal_soma/0/pyr_soma_m_out_b_out/v" scale="1 mV" color="#000000"/>
+        </Display>
+    
+        <Display id="GraphWin_12" title="ACnet2: TestSoma, pyramidal_soma, Ca_conc:CONC:ca" xmin="-70.0" xmax="770.0" ymin="-1E-5" ymax="9E-5" timeScale="1ms">
+            <Line id="Ca_conc_CONC_ca-pyramidal_soma_0" timeScale="1ms" quantity="pyramidal_soma/0/pyr_soma_m_out_b_out/caConc" scale="1 mol_per_cm3" color="#000000"/>
+        </Display>
+    
+    
+        <OutputFile id="pyramidal_soma_v_OF" fileName="pyramidal_soma_0.dat">
+            <OutputColumn id="v" quantity="pyramidal_soma/0/pyr_soma_m_out_b_out/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_ca_2_OF" fileName="pyramidal_soma_0.Ca_conc_CONC_ca.dat">
+            <OutputColumn id="caConc" quantity="pyramidal_soma/0/pyr_soma_m_out_b_out/caConc"/>
+        </OutputFile>
+    </Component>
+
+
+</Lems>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/LEMS_pyrfull_in.xml b/LEMSexamples/morphologies/LEMS_pyrfull_in.xml
new file mode 100644
index 0000000..32a9647
--- /dev/null
+++ b/LEMSexamples/morphologies/LEMS_pyrfull_in.xml
@@ -0,0 +1,92 @@
+<Lems xmlns="http://www.neuroml.org/lems/0.7.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/lems/0.7.2  https://raw.githubusercontent.com/LEMS/LEMS/development/Schemas/LEMS/LEMS_v0.7.2.xsd">
+
+    <Target component="sim1" reportFile="simulator.props" timesFile="time.dat"/>
+
+        <!--Include standard NeuroML 2 ComponentType definitions-->
+
+    <Include file="Cells.xml"/>
+    <Include file="Networks.xml"/>
+    <Include file="Simulation.xml"/>
+
+    
+
+        <!--Include the generated NeuroML 2 files-->
+
+
+    <Include file="pyr_4_sym.cell.nml"/>
+    <Include file="pyrfull_in.net.nml"/>
+
+    
+
+        <!--Note: this could be: Simulation id="sim1" ... , but Component type="Simulation" ... 
+        is used to allow validation of this file according to the LEMS schema specified above...-->
+    <Component type="Simulation" id="sim1" length="700.0ms" step="0.01ms" target="network">
+        
+    
+        <Display id="GraphWin_12" title="ACnet2: Default Simulation Configuration, pyramidals, Ca_conc:CONC:ca" xmin="-0.07" xmax="0.77000004" ymin="-12.000001" ymax="132.0" timeScale="1s">
+            <Line id="pyramidals_0 Ca_conc_CONC_ca" timeScale="1s" quantity="pyramidals/0/pyr_4_sym/0/caConc" scale="1 mol_per_m3" color="#000000"/>
+        </Display>
+    
+        <Display id="pyramidals_v" title="ACnet2: Default Simulation Configuration, pyramidals, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE" xmin="-0.07" xmax="0.77000004" ymin="-0.104" ymax="0.064" timeScale="1s">
+            <Line id="pyramidals_0_0 v" timeScale="1s" quantity="pyramidals/0/pyr_4_sym/0/v" scale="1 V" color="#000000"/>
+        
+            <Line id="pyramidals_0_1 v" timeScale="1s" quantity="pyramidals/0/pyr_4_sym/1/v" scale="1 V" color="#ff0000"/>
+        
+            <Line id="pyramidals_0_2 v" timeScale="1s" quantity="pyramidals/0/pyr_4_sym/2/v" scale="1 V" color="#0000ff"/>
+        
+            <Line id="pyramidals_0_3 v" timeScale="1s" quantity="pyramidals/0/pyr_4_sym/3/v" scale="1 V" color="#009b00"/>
+        
+            <Line id="pyramidals_0_4 v" timeScale="1s" quantity="pyramidals/0/pyr_4_sym/4/v" scale="1 V" color="#ffc800"/>
+        
+            <Line id="pyramidals_0_5 v" timeScale="1s" quantity="pyramidals/0/pyr_4_sym/5/v" scale="1 V" color="#8c6400"/>
+        
+            <Line id="pyramidals_0_6 v" timeScale="1s" quantity="pyramidals/0/pyr_4_sym/6/v" scale="1 V" color="#ff00ff"/>
+        
+            <Line id="pyramidals_0_7 v" timeScale="1s" quantity="pyramidals/0/pyr_4_sym/7/v" scale="1 V" color="#ffff00"/>
+        
+            <Line id="pyramidals_0_8 v" timeScale="1s" quantity="pyramidals/0/pyr_4_sym/8/v" scale="1 V" color="#808080"/>
+        </Display>
+    
+        <OutputFile id="pyramidals_ca_0_0_OF" fileName="pyramidals_0.0.Ca_conc_CONC_ca.dat">
+            <OutputColumn id="caConc" quantity="pyramidals/0/pyr_4_sym/0/caConc"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_0_OF" fileName="pyramidals_0.0.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_4_sym/0/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_1_OF" fileName="pyramidals_0.1.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_4_sym/1/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_2_OF" fileName="pyramidals_0.2.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_4_sym/2/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_3_OF" fileName="pyramidals_0.3.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_4_sym/3/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_4_OF" fileName="pyramidals_0.4.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_4_sym/4/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_5_OF" fileName="pyramidals_0.5.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_4_sym/5/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_6_OF" fileName="pyramidals_0.6.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_4_sym/6/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_7_OF" fileName="pyramidals_0.7.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_4_sym/7/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_8_OF" fileName="pyramidals_0.8.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_4_sym/8/v"/>
+        </OutputFile>
+    </Component>
+
+
+</Lems>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/LEMS_pyrfull_out.xml b/LEMSexamples/morphologies/LEMS_pyrfull_out.xml
new file mode 100644
index 0000000..e91c7c7
--- /dev/null
+++ b/LEMSexamples/morphologies/LEMS_pyrfull_out.xml
@@ -0,0 +1,91 @@
+<Lems xmlns="http://www.neuroml.org/lems/0.7.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/lems/0.7.2  https://raw.githubusercontent.com/LEMS/LEMS/development/Schemas/LEMS/LEMS_v0.7.2.xsd">
+
+    <Target component="sim1" reportFile="simulator.props" timesFile="time.dat"/>
+
+        <!--Include standard NeuroML 2 ComponentType definitions-->
+
+    <Include file="Cells.xml"/>
+    <Include file="Networks.xml"/>
+    <Include file="Simulation.xml"/>
+
+    
+
+        <!--Include the generated NeuroML 2 files-->
+
+
+    <Include file="pyrfull_out.net.nml"/>
+
+    
+
+        <!--Note: this could be: Simulation id="sim1" ... , but Component type="Simulation" ... 
+        is used to allow validation of this file according to the LEMS schema specified above...-->
+    <Component type="Simulation" id="sim1" length="700.0ms" step="0.01ms" target="network">
+        
+    
+        <Display id="GraphWin_12" title="ACnet2: Default Simulation Configuration, pyramidals, Ca_conc:CONC:ca" xmin="-0.07" xmax="0.77000004" ymin="-12.000001" ymax="132.0" timeScale="1s">
+            <Line id="pyramidals_0 Ca_conc_CONC_ca" timeScale="1s" quantity="pyramidals/0/pyr_full_out/0/caConc" scale="1 mol_per_m3" color="#000000"/>
+        </Display>
+    
+        <Display id="pyramidals_v" title="ACnet2: Default Simulation Configuration, pyramidals, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE, VOLTAGE" xmin="-0.07" xmax="0.77000004" ymin="-0.104" ymax="0.064" timeScale="1s">
+            <Line id="pyramidals_0_0 v" timeScale="1s" quantity="pyramidals/0/pyr_full_out/0/v" scale="1 V" color="#000000"/>
+        
+            <Line id="pyramidals_0_1 v" timeScale="1s" quantity="pyramidals/0/pyr_full_out/1/v" scale="1 V" color="#ff0000"/>
+        
+            <Line id="pyramidals_0_2 v" timeScale="1s" quantity="pyramidals/0/pyr_full_out/2/v" scale="1 V" color="#0000ff"/>
+        
+            <Line id="pyramidals_0_3 v" timeScale="1s" quantity="pyramidals/0/pyr_full_out/3/v" scale="1 V" color="#009b00"/>
+        
+            <Line id="pyramidals_0_4 v" timeScale="1s" quantity="pyramidals/0/pyr_full_out/4/v" scale="1 V" color="#ffc800"/>
+        
+            <Line id="pyramidals_0_5 v" timeScale="1s" quantity="pyramidals/0/pyr_full_out/5/v" scale="1 V" color="#8c6400"/>
+        
+            <Line id="pyramidals_0_6 v" timeScale="1s" quantity="pyramidals/0/pyr_full_out/6/v" scale="1 V" color="#ff00ff"/>
+        
+            <Line id="pyramidals_0_7 v" timeScale="1s" quantity="pyramidals/0/pyr_full_out/7/v" scale="1 V" color="#ffff00"/>
+        
+            <Line id="pyramidals_0_8 v" timeScale="1s" quantity="pyramidals/0/pyr_full_out/8/v" scale="1 V" color="#808080"/>
+        </Display>
+    
+        <OutputFile id="pyramidals_ca_0_0_OF" fileName="pyramidals_0.0.Ca_conc_CONC_ca.dat">
+            <OutputColumn id="caConc" quantity="pyramidals/0/pyr_full_out/0/caConc"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_0_OF" fileName="pyramidals_0.0.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_full_out/0/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_1_OF" fileName="pyramidals_0.1.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_full_out/1/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_2_OF" fileName="pyramidals_0.2.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_full_out/2/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_3_OF" fileName="pyramidals_0.3.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_full_out/3/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_4_OF" fileName="pyramidals_0.4.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_full_out/4/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_5_OF" fileName="pyramidals_0.5.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_full_out/5/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_6_OF" fileName="pyramidals_0.6.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_full_out/6/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_7_OF" fileName="pyramidals_0.7.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_full_out/7/v"/>
+        </OutputFile>
+    
+        <OutputFile id="pyramidals_v_0_8_OF" fileName="pyramidals_0.8.dat">
+            <OutputColumn id="v" quantity="pyramidals/0/pyr_full_out/8/v"/>
+        </OutputFile>
+    </Component>
+
+
+</Lems>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/LeakConductance_pyr.channel.nml b/LEMSexamples/morphologies/LeakConductance_pyr.channel.nml
new file mode 100644
index 0000000..ecfb8b7
--- /dev/null
+++ b/LEMSexamples/morphologies/LeakConductance_pyr.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="LeakConductance_pyr">
+        
+    <notes>NeuroML file containing a single Channel description</notes>
+        
+    <ionChannel id="LeakConductance_pyr" conductance="10pS" type="ionChannelPassive">
+                
+        <notes>Passive conductance for pyramidal cell</notes>
+                                    
+    
+    </ionChannel>
+    
+</neuroml>
diff --git a/LEMSexamples/morphologies/Na_pyr.channel.nml b/LEMSexamples/morphologies/Na_pyr.channel.nml
new file mode 100644
index 0000000..5d0ff83
--- /dev/null
+++ b/LEMSexamples/morphologies/Na_pyr.channel.nml
@@ -0,0 +1,68 @@
+<?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="Na_pyr">
+        
+    <notes>NeuroML file containing a single Sodium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+        
+    <ionChannel id="Na_pyr" conductance="10pS" type="ionChannelHH" species="na">
+                
+        <notes>NeuroML file containing a single Sodium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+                        
+        
+        <annotation>
+                        
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                                
+                <rdf:Description rdf:about="Na_pyr">
+                                        
+                    
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                                                
+                        <rdf:Bag>
+                                                        
+                            <rdf:li>Traub, R. D., Wong, R. K., Miles, R., and Michelson, H. (1991). A model of a CA3 hippocampal pyramidal neuron incorporating voltage-clamp data on intrinsic conductances. Journal of neurophysiology, 66(2), 635-50.</rdf:li>
+                                                        
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/1663538"/>
+                                                    
+                        </rdf:Bag>
+                                            
+                    </bqmodel:isDescribedBy>
+                                    
+                    
+                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                                                
+                        <rdf:Bag>
+                                                        
+                            <rdf:li>Na channels</rdf:li>
+                                                        
+                            <rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/NeuronProp.aspx?id=259&amp;mo=1&amp;re=&amp;pr=C"/>
+                                                    
+                        </rdf:Bag>
+                                            
+                    </bqbiol:isVersionOf>
+                                    
+                </rdf:Description>
+                            
+            </rdf:RDF>
+                    
+        </annotation>
+                
+        <gate id="m" type="gateHHrates" instances="2">
+                        
+            <forwardRate type="HHExpLinearRate" rate="1.28e3per_s" scale="0.004V" midpoint="-4.69e-2V"/>
+                        
+            <reverseRate type="HHExpLinearRate" rate="1.4e3per_s" scale="-0.005V" midpoint="-19.9e-3V"/>
+                    
+        </gate>
+                
+        <gate id="h" type="gateHHrates" instances="1">
+                        
+            <forwardRate type="HHExpRate" rate="1.28e2per_s" scale="-0.018V" midpoint="-4.3e-2V"/>
+                        
+            <reverseRate type="HHSigmoidRate" rate="4e3per_s" scale="0.005V" midpoint="-2e-2V"/>
+                    
+        </gate>
+                                    
+    
+    </ionChannel>
+    
+</neuroml>
diff --git a/LEMSexamples/morphologies/README.md b/LEMSexamples/morphologies/README.md
new file mode 100644
index 0000000..5bd53d5
--- /dev/null
+++ b/LEMSexamples/morphologies/README.md
@@ -0,0 +1,47 @@
+## Examples with tests for various ways to include `<morphology>` and `<biophysicalProperties>` in `<cell>`
+
+
+See https://github.com/NeuroML/NeuroML2/issues/150 for background.
+
+Cells with morphologies and biophysical properties can be expressed as:
+
+```xml
+    <cell id="pyr_soma_m_in_b_in">
+...
+        <morphology id="morph0">
+
+            <segment ...>
+            ...
+
+        </morphology>
+
+        <biophysicalProperties id="biophys1">
+        ...
+        </biophysicalProperties>
+
+    </cell>
+```
+or
+```xml
+    <cell id="pyr_soma_m_out_b_out" morphology="morph0" biophysicalProperties="biophys1">
+        ...
+    </cell>
+
+    <!-- Potentially in other files... -->
+
+    <morphology id="morph0">
+
+        <segment ...>
+        ...
+
+    </morphology>
+
+    <biophysicalProperties id="biophys1">
+    ...
+    </biophysicalProperties>
+
+```
+See [pyr_soma_m_in_b_in.cell.nml](pyr_soma_m_in_b_in.cell.nml), [pyr_soma_m_out_b_in.cell.nml](pyr_soma_m_out_b_in.cell.nml), [pyr_soma_m_in_b_out.cell.nml](pyr_soma_m_in_b_out.cell.nml), [pyr_full_out.cell.nml](pyr_full_out.cell.nml) etc.
+
+
+
diff --git a/LEMSexamples/morphologies/network_m_out_b_out.net.nml b/LEMSexamples/morphologies/network_m_out_b_out.net.nml
new file mode 100644
index 0000000..5b89a3d
--- /dev/null
+++ b/LEMSexamples/morphologies/network_m_out_b_out.net.nml
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="pyr_4_sym_soma">
+
+
+        <!--   Cell files-->
+    <include href="pyr_soma_m_out_b_out.cell.nml"/>
+
+    <pulseGenerator id="Input_3" delay="100.0ms" duration="500.0ms" amplitude="2.0E-4uA"/>
+
+    <network id="network" type="networkWithTemperature" temperature="6.3 degC">
+
+        <population id="pyramidal_soma" component="pyr_soma_m_out_b_out" type="populationList" size="1">
+           <annotation>
+                <property tag="color" value="0.7421875 0.07421875 0.95703125"/>
+            </annotation>
+            <instance id="0">
+                <location x="400.0" y="0.0" z="0.0"/>
+            </instance>
+        </population>
+
+        <inputList id="Input_3" component="Input_3" population="pyramidal_soma">
+            <input id="0" target="../pyramidal_soma/0/pyr_soma_m_out_b_out" destination="synapses"/>
+        </inputList>
+
+
+    </network>
+    
+
+</neuroml>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/pyr_4_sym.cell.nml b/LEMSexamples/morphologies/pyr_4_sym.cell.nml
new file mode 100644
index 0000000..dda6278
--- /dev/null
+++ b/LEMSexamples/morphologies/pyr_4_sym.cell.nml
@@ -0,0 +1,246 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="pyr_4_sym">
+
+    <include href="Ca_conc.nml"/>
+
+    <include href="Ca_pyr.channel.nml"/>
+
+    <include href="Kahp_pyr.channel.nml"/>
+
+    <include href="Kdr_pyr.channel.nml"/>
+
+    <include href="LeakConductance_pyr.channel.nml"/>
+
+    <include href="Na_pyr.channel.nml"/>
+
+    <cell id="pyr_4_sym">
+
+        <notes>A simplified pyramidal cell model with 9 compartments</notes>
+
+        <morphology id="morphology_pyr_4_sym">
+
+            <segment id="0" name="soma">
+                <proximal x="0.0" y="0.0" z="0.0" diameter="23.0"/>
+                <distal x="0.0" y="17.0" z="0.0" diameter="23.0"/>
+            </segment>
+
+            <segment id="1" name="apical0">
+                <parent segment="0"/>
+                <proximal x="0.0" y="17.0" z="0.0" diameter="6.0"/>
+                <distal x="0.0" y="77.0" z="0.0" diameter="6.0"/>
+            </segment>
+
+            <segment id="2" name="apical2">
+                <parent segment="1"/>
+                <proximal x="0.0" y="77.0" z="0.0" diameter="4.4"/>
+                <distal x="0.0" y="477.0" z="0.0" diameter="4.4"/>
+            </segment>
+
+            <segment id="3" name="apical3">
+                <parent segment="2"/>
+                <proximal x="0.0" y="477.0" z="0.0" diameter="2.9"/>
+                <distal x="0.0" y="877.0" z="0.0" diameter="2.9"/>
+            </segment>
+
+            <segment id="4" name="apical4">
+                <parent segment="3"/>
+                <proximal x="0.0" y="877.0" z="0.0" diameter="2.0"/>
+                <distal x="0.0" y="1127.0" z="0.0" diameter="2.0"/>
+            </segment>
+
+            <segment id="5" name="apical1">
+                <parent segment="1"/>
+                <proximal x="0.0" y="77.0" z="0.0" diameter="3.0"/>
+                <distal x="-150.0" y="77.0" z="0.0" diameter="3.0"/>
+            </segment>
+
+            <segment id="6" name="basal0">
+                <parent segment="0" fractionAlong="0.0"/>
+                <proximal x="0.0" y="0.0" z="0.0" diameter="4.0"/>
+                <distal x="0.0" y="-50.0" z="0.0" diameter="4.0"/>
+            </segment>
+
+            <segment id="7" name="basal1">
+                <parent segment="6"/>
+                <proximal x="0.0" y="-50.0" z="0.0" diameter="5.0"/>
+                <distal x="106.07" y="-156.07" z="0.0" diameter="5.0"/>
+            </segment>
+
+            <segment id="8" name="basal2">
+                <parent segment="6"/>
+                <proximal x="0.0" y="-50.0" z="0.0" diameter="5.0"/>
+                <distal x="-106.07" y="-156.07" z="0.0" diameter="5.0"/>
+            </segment>
+
+            <segmentGroup id="soma" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="0"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical0" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="1"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical2" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="2"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical3" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="3"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical4" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="4"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical1" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="5"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal0" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="6"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal1" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="7"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal2" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="8"/>
+            </segmentGroup>
+
+            <segmentGroup id="all">
+                <include segmentGroup="soma"/>
+                <include segmentGroup="apical0"/>
+                <include segmentGroup="apical2"/>
+                <include segmentGroup="apical3"/>
+                <include segmentGroup="apical4"/>
+                <include segmentGroup="apical1"/>
+                <include segmentGroup="basal0"/>
+                <include segmentGroup="basal1"/>
+                <include segmentGroup="basal2"/>
+            </segmentGroup>
+
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">    <!--Soma group-->
+
+                <include segmentGroup="soma"/>
+            </segmentGroup>
+
+            <segmentGroup id="dendrite_group" neuroLexId="GO:0030425">    <!--Dendrite group-->
+
+                <include segmentGroup="apical0"/>
+                <include segmentGroup="apical2"/>
+                <include segmentGroup="apical3"/>
+                <include segmentGroup="apical4"/>
+                <include segmentGroup="apical1"/>
+                <include segmentGroup="basal0"/>
+                <include segmentGroup="basal1"/>
+                <include segmentGroup="basal2"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical_dends">
+                <include segmentGroup="apical0"/>
+                <include segmentGroup="apical2"/>
+                <include segmentGroup="apical3"/>
+                <include segmentGroup="apical4"/>
+                <include segmentGroup="apical1"/>
+            </segmentGroup>
+
+            <segmentGroup id="middle_apical_dendrite">
+                <include segmentGroup="apical3"/>
+            </segmentGroup>
+
+            <segmentGroup id="thalamic_input">
+                <include segmentGroup="apical1"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal_dends">
+                <include segmentGroup="basal0"/>
+                <include segmentGroup="basal1"/>
+                <include segmentGroup="basal2"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal_gaba_input">
+                <include segmentGroup="basal0"/>
+            </segmentGroup>
+
+            <segmentGroup id="background_input">
+                <include segmentGroup="basal1"/>
+            </segmentGroup>
+
+            
+        </morphology>
+
+            <!--Adding the biophysical parameters-->
+
+        <biophysicalProperties id="biophys">
+
+            <membraneProperties>
+                
+                <channelDensity condDensity="10.0 mS_per_cm2" id="Ca_pyr_soma_group" ionChannel="Ca_pyr" segmentGroup="soma_group" ion="ca" erev="80.0 mV"/>
+                
+                <channelDensity condDensity="2.5 mS_per_cm2" id="Kahp_pyr_soma_group" ionChannel="Kahp_pyr" segmentGroup="soma_group" ion="k" erev="-75.0 mV"/>
+                
+                <channelDensity condDensity="80.0 mS_per_cm2" id="Kdr_pyr_soma_group" ionChannel="Kdr_pyr" segmentGroup="soma_group" ion="k" erev="-75.0 mV"/>
+                
+                <channelDensity condDensity="0.1420051 mS_per_cm2" id="LeakConductance_pyr_all" ionChannel="LeakConductance_pyr" erev="-66.0 mV" ion="non_specific"/>
+                
+                <channelDensity condDensity="120.0 mS_per_cm2" id="Na_pyr_soma_group" ionChannel="Na_pyr" segmentGroup="soma_group" ion="na" erev="55.0 mV"/>
+                
+
+                <spikeThresh value="0 mV"/>
+
+                <specificCapacitance value="2.84 uF_per_cm2"/>
+
+                <initMembPotential value="-65.0 mV"/>
+
+            </membraneProperties>
+
+            <intracellularProperties>
+
+                <species segmentGroup="soma_group" id="ca" ion="ca" concentrationModel="Ca_conc" initialConcentration="5.0E-11 mol_per_cm3" initialExtConcentration="3.0E-6 mol_per_cm3"/>
+
+                <resistivity value="0.2 kohm_cm"/>
+
+            </intracellularProperties>
+
+        </biophysicalProperties>
+
+    </cell>
+    
+</neuroml>
diff --git a/LEMSexamples/morphologies/pyr_4_sym_soma_morph.nml b/LEMSexamples/morphologies/pyr_4_sym_soma_morph.nml
new file mode 100644
index 0000000..9154b8a
--- /dev/null
+++ b/LEMSexamples/morphologies/pyr_4_sym_soma_morph.nml
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="pyr_4_sym_soma">
+
+
+
+    <morphology id="morphology_pyr_soma">
+
+        <segment id="0" name="soma">
+            <proximal x="0.0" y="0.0" z="0.0" diameter="23.0"/>
+            <distal x="0.0" y="17.0" z="0.0" diameter="23.0"/>
+        </segment>
+
+        <segmentGroup id="soma" neuroLexId="sao864921383">    <!--
+            This group contains an unbranched set of segments, and all of the segmentGroups marked with
+            neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+            These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+            <member segment="0"/>
+        </segmentGroup>
+
+        <segmentGroup id="all">
+            <include segmentGroup="soma"/>
+        </segmentGroup>
+
+        <segmentGroup id="soma_group" neuroLexId="GO:0043025">    <!--Soma group-->
+
+            <include segmentGroup="soma"/>
+        </segmentGroup>
+
+    </morphology>
+
+
+</neuroml>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/pyr_biophysics.nml b/LEMSexamples/morphologies/pyr_biophysics.nml
new file mode 100644
index 0000000..b90938d
--- /dev/null
+++ b/LEMSexamples/morphologies/pyr_biophysics.nml
@@ -0,0 +1,50 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="pyr_4_sym_soma">
+
+    <include href="Ca_conc.nml"/>
+
+    <include href="Ca_pyr.channel.nml"/>
+
+    <include href="Kahp_pyr.channel.nml"/>
+
+    <include href="Kdr_pyr.channel.nml"/>
+
+    <include href="LeakConductance_pyr.channel.nml"/>
+
+    <include href="Na_pyr.channel.nml"/>
+
+        <biophysicalProperties id="biophys">
+
+            <membraneProperties>
+                
+                <channelDensity condDensity="10.0 mS_per_cm2" id="Ca_pyr_soma_group" ionChannel="Ca_pyr" segmentGroup="soma_group" ion="ca" erev="80.0 mV"/>
+                
+                <channelDensity condDensity="2.5 mS_per_cm2" id="Kahp_pyr_soma_group" ionChannel="Kahp_pyr" segmentGroup="soma_group" ion="k" erev="-75.0 mV"/>
+                
+                <channelDensity condDensity="80.0 mS_per_cm2" id="Kdr_pyr_soma_group" ionChannel="Kdr_pyr" segmentGroup="soma_group" ion="k" erev="-75.0 mV"/>
+                
+                <channelDensity condDensity="0.1420051 mS_per_cm2" id="LeakConductance_pyr_all" ionChannel="LeakConductance_pyr" erev="-66.0 mV" ion="non_specific"/>
+                
+                <channelDensity condDensity="120.0 mS_per_cm2" id="Na_pyr_soma_group" ionChannel="Na_pyr" segmentGroup="soma_group" ion="na" erev="55.0 mV"/>
+                
+
+                <spikeThresh value="0.0 mV"/>
+
+                <specificCapacitance value="2.84 uF_per_cm2"/>
+
+                <initMembPotential value="-65.0 mV"/>
+
+            </membraneProperties>
+
+            <intracellularProperties>
+
+                <species id="ca" ion="ca" concentrationModel="Ca_conc" initialConcentration="5.0E-11 mol_per_cm3" initialExtConcentration="3.0E-6 mol_per_cm3"/>
+
+                <resistivity value="0.2 kohm_cm"/>
+
+            </intracellularProperties>
+
+        </biophysicalProperties>
+
+    
+</neuroml>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/pyr_full_morph_biophys.nml b/LEMSexamples/morphologies/pyr_full_morph_biophys.nml
new file mode 100644
index 0000000..28a2561
--- /dev/null
+++ b/LEMSexamples/morphologies/pyr_full_morph_biophys.nml
@@ -0,0 +1,241 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="pyr_4_sym">
+
+    <include href="Ca_conc.nml"/>
+
+    <include href="Ca_pyr.channel.nml"/>
+
+    <include href="Kahp_pyr.channel.nml"/>
+
+    <include href="Kdr_pyr.channel.nml"/>
+
+    <include href="LeakConductance_pyr.channel.nml"/>
+
+    <include href="Na_pyr.channel.nml"/>
+
+
+        <morphology id="morphology_pyr_4_sym">
+
+            <segment id="0" name="soma">
+                <proximal x="0.0" y="0.0" z="0.0" diameter="23.0"/>
+                <distal x="0.0" y="17.0" z="0.0" diameter="23.0"/>
+            </segment>
+
+            <segment id="1" name="apical0">
+                <parent segment="0"/>
+                <proximal x="0.0" y="17.0" z="0.0" diameter="6.0"/>
+                <distal x="0.0" y="77.0" z="0.0" diameter="6.0"/>
+            </segment>
+
+            <segment id="2" name="apical2">
+                <parent segment="1"/>
+                <proximal x="0.0" y="77.0" z="0.0" diameter="4.4"/>
+                <distal x="0.0" y="477.0" z="0.0" diameter="4.4"/>
+            </segment>
+
+            <segment id="3" name="apical3">
+                <parent segment="2"/>
+                <proximal x="0.0" y="477.0" z="0.0" diameter="2.9"/>
+                <distal x="0.0" y="877.0" z="0.0" diameter="2.9"/>
+            </segment>
+
+            <segment id="4" name="apical4">
+                <parent segment="3"/>
+                <proximal x="0.0" y="877.0" z="0.0" diameter="2.0"/>
+                <distal x="0.0" y="1127.0" z="0.0" diameter="2.0"/>
+            </segment>
+
+            <segment id="5" name="apical1">
+                <parent segment="1"/>
+                <proximal x="0.0" y="77.0" z="0.0" diameter="3.0"/>
+                <distal x="-150.0" y="77.0" z="0.0" diameter="3.0"/>
+            </segment>
+
+            <segment id="6" name="basal0">
+                <parent segment="0" fractionAlong="0.0"/>
+                <proximal x="0.0" y="0.0" z="0.0" diameter="4.0"/>
+                <distal x="0.0" y="-50.0" z="0.0" diameter="4.0"/>
+            </segment>
+
+            <segment id="7" name="basal1">
+                <parent segment="6"/>
+                <proximal x="0.0" y="-50.0" z="0.0" diameter="5.0"/>
+                <distal x="106.07" y="-156.07" z="0.0" diameter="5.0"/>
+            </segment>
+
+            <segment id="8" name="basal2">
+                <parent segment="6"/>
+                <proximal x="0.0" y="-50.0" z="0.0" diameter="5.0"/>
+                <distal x="-106.07" y="-156.07" z="0.0" diameter="5.0"/>
+            </segment>
+
+            <segmentGroup id="soma" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="0"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical0" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="1"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical2" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="2"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical3" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="3"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical4" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="4"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical1" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="5"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal0" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="6"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal1" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="7"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal2" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="8"/>
+            </segmentGroup>
+
+            <segmentGroup id="all">
+                <include segmentGroup="soma"/>
+                <include segmentGroup="apical0"/>
+                <include segmentGroup="apical2"/>
+                <include segmentGroup="apical3"/>
+                <include segmentGroup="apical4"/>
+                <include segmentGroup="apical1"/>
+                <include segmentGroup="basal0"/>
+                <include segmentGroup="basal1"/>
+                <include segmentGroup="basal2"/>
+            </segmentGroup>
+
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">    <!--Soma group-->
+
+                <include segmentGroup="soma"/>
+            </segmentGroup>
+
+            <segmentGroup id="dendrite_group" neuroLexId="GO:0030425">    <!--Dendrite group-->
+
+                <include segmentGroup="apical0"/>
+                <include segmentGroup="apical2"/>
+                <include segmentGroup="apical3"/>
+                <include segmentGroup="apical4"/>
+                <include segmentGroup="apical1"/>
+                <include segmentGroup="basal0"/>
+                <include segmentGroup="basal1"/>
+                <include segmentGroup="basal2"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical_dends">
+                <include segmentGroup="apical0"/>
+                <include segmentGroup="apical2"/>
+                <include segmentGroup="apical3"/>
+                <include segmentGroup="apical4"/>
+                <include segmentGroup="apical1"/>
+            </segmentGroup>
+
+            <segmentGroup id="middle_apical_dendrite">
+                <include segmentGroup="apical3"/>
+            </segmentGroup>
+
+            <segmentGroup id="thalamic_input">
+                <include segmentGroup="apical1"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal_dends">
+                <include segmentGroup="basal0"/>
+                <include segmentGroup="basal1"/>
+                <include segmentGroup="basal2"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal_gaba_input">
+                <include segmentGroup="basal0"/>
+            </segmentGroup>
+
+            <segmentGroup id="background_input">
+                <include segmentGroup="basal1"/>
+            </segmentGroup>
+
+            
+        </morphology>
+
+            <!--Adding the biophysical parameters-->
+
+        <biophysicalProperties id="biophys">
+
+            <membraneProperties>
+                
+                <channelDensity condDensity="10.0 mS_per_cm2" id="Ca_pyr_soma_group" ionChannel="Ca_pyr" segmentGroup="soma_group" ion="ca" erev="80.0 mV"/>
+                
+                <channelDensity condDensity="2.5 mS_per_cm2" id="Kahp_pyr_soma_group" ionChannel="Kahp_pyr" segmentGroup="soma_group" ion="k" erev="-75.0 mV"/>
+                
+                <channelDensity condDensity="80.0 mS_per_cm2" id="Kdr_pyr_soma_group" ionChannel="Kdr_pyr" segmentGroup="soma_group" ion="k" erev="-75.0 mV"/>
+                
+                <channelDensity condDensity="0.1420051 mS_per_cm2" id="LeakConductance_pyr_all" ionChannel="LeakConductance_pyr" erev="-66.0 mV" ion="non_specific"/>
+                
+                <channelDensity condDensity="120.0 mS_per_cm2" id="Na_pyr_soma_group" ionChannel="Na_pyr" segmentGroup="soma_group" ion="na" erev="55.0 mV"/>
+                
+
+                <spikeThresh value="0 mV"/>
+
+                <specificCapacitance value="2.84 uF_per_cm2"/>
+
+                <initMembPotential value="-65.0 mV"/>
+
+            </membraneProperties>
+
+            <intracellularProperties>
+
+                <species segmentGroup="soma_group" id="ca" ion="ca" concentrationModel="Ca_conc" initialConcentration="5.0E-11 mol_per_cm3" initialExtConcentration="3.0E-6 mol_per_cm3"/>
+
+                <resistivity value="0.2 kohm_cm"/>
+
+            </intracellularProperties>
+
+        </biophysicalProperties>
+    
+</neuroml>
diff --git a/LEMSexamples/morphologies/pyr_full_out.cell.nml b/LEMSexamples/morphologies/pyr_full_out.cell.nml
new file mode 100644
index 0000000..9d335f5
--- /dev/null
+++ b/LEMSexamples/morphologies/pyr_full_out.cell.nml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="pyr_4_sym">
+
+    <include href="pyr_full_morph_biophys.nml"/>
+
+
+    <cell id="pyr_full_out"  morphology="morphology_pyr_4_sym" biophysicalProperties="biophys">
+
+        <notes>A simplified pyramidal cell model with 9 compartments</notes>
+        
+    </cell>
+    
+</neuroml>
diff --git a/LEMSexamples/morphologies/pyr_morphology.cell.nml b/LEMSexamples/morphologies/pyr_morphology.cell.nml
new file mode 100644
index 0000000..9590c14
--- /dev/null
+++ b/LEMSexamples/morphologies/pyr_morphology.cell.nml
@@ -0,0 +1,201 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="pyr_4_sym">
+
+
+
+    <cell id="pyr_morphology">
+
+        <notes>Just the morphology</notes>
+
+        <morphology id="morph">
+
+            <segment id="0" name="soma">
+                <proximal x="0.0" y="0.0" z="0.0" diameter="23.0"/>
+                <distal x="0.0" y="17.0" z="0.0" diameter="23.0"/>
+            </segment>
+
+            <segment id="1" name="apical0">
+                <parent segment="0"/>
+                <proximal x="0.0" y="17.0" z="0.0" diameter="6.0"/>
+                <distal x="0.0" y="77.0" z="0.0" diameter="6.0"/>
+            </segment>
+
+            <segment id="2" name="apical2">
+                <parent segment="1"/>
+                <proximal x="0.0" y="77.0" z="0.0" diameter="4.4"/>
+                <distal x="0.0" y="477.0" z="0.0" diameter="4.4"/>
+            </segment>
+
+            <segment id="3" name="apical3">
+                <parent segment="2"/>
+                <proximal x="0.0" y="477.0" z="0.0" diameter="2.9"/>
+                <distal x="0.0" y="877.0" z="0.0" diameter="2.9"/>
+            </segment>
+
+            <segment id="4" name="apical4">
+                <parent segment="3"/>
+                <proximal x="0.0" y="877.0" z="0.0" diameter="2.0"/>
+                <distal x="0.0" y="1127.0" z="0.0" diameter="2.0"/>
+            </segment>
+
+            <segment id="5" name="apical1">
+                <parent segment="1"/>
+                <proximal x="0.0" y="77.0" z="0.0" diameter="3.0"/>
+                <distal x="-150.0" y="77.0" z="0.0" diameter="3.0"/>
+            </segment>
+
+            <segment id="6" name="basal0">
+                <parent segment="0" fractionAlong="0.0"/>
+                <proximal x="0.0" y="0.0" z="0.0" diameter="4.0"/>
+                <distal x="0.0" y="-50.0" z="0.0" diameter="4.0"/>
+            </segment>
+
+            <segment id="7" name="basal1">
+                <parent segment="6"/>
+                <proximal x="0.0" y="-50.0" z="0.0" diameter="5.0"/>
+                <distal x="106.07" y="-156.07" z="0.0" diameter="5.0"/>
+            </segment>
+
+            <segment id="8" name="basal2">
+                <parent segment="6"/>
+                <proximal x="0.0" y="-50.0" z="0.0" diameter="5.0"/>
+                <distal x="-106.07" y="-156.07" z="0.0" diameter="5.0"/>
+            </segment>
+
+            <segmentGroup id="soma" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="0"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical0" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="1"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical2" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="2"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical3" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="3"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical4" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="4"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical1" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="5"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal0" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="6"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal1" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="7"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal2" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="8"/>
+            </segmentGroup>
+
+            <segmentGroup id="all">
+                <include segmentGroup="soma"/>
+                <include segmentGroup="apical0"/>
+                <include segmentGroup="apical2"/>
+                <include segmentGroup="apical3"/>
+                <include segmentGroup="apical4"/>
+                <include segmentGroup="apical1"/>
+                <include segmentGroup="basal0"/>
+                <include segmentGroup="basal1"/>
+                <include segmentGroup="basal2"/>
+            </segmentGroup>
+
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">    <!--Soma group-->
+
+                <include segmentGroup="soma"/>
+            </segmentGroup>
+
+            <segmentGroup id="dendrite_group" neuroLexId="GO:0030425">    <!--Dendrite group-->
+
+                <include segmentGroup="apical0"/>
+                <include segmentGroup="apical2"/>
+                <include segmentGroup="apical3"/>
+                <include segmentGroup="apical4"/>
+                <include segmentGroup="apical1"/>
+                <include segmentGroup="basal0"/>
+                <include segmentGroup="basal1"/>
+                <include segmentGroup="basal2"/>
+            </segmentGroup>
+
+            <segmentGroup id="apical_dends">
+                <include segmentGroup="apical0"/>
+                <include segmentGroup="apical2"/>
+                <include segmentGroup="apical3"/>
+                <include segmentGroup="apical4"/>
+                <include segmentGroup="apical1"/>
+            </segmentGroup>
+
+            <segmentGroup id="middle_apical_dendrite">
+                <include segmentGroup="apical3"/>
+            </segmentGroup>
+
+            <segmentGroup id="thalamic_input">
+                <include segmentGroup="apical1"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal_dends">
+                <include segmentGroup="basal0"/>
+                <include segmentGroup="basal1"/>
+                <include segmentGroup="basal2"/>
+            </segmentGroup>
+
+            <segmentGroup id="basal_gaba_input">
+                <include segmentGroup="basal0"/>
+            </segmentGroup>
+
+            <segmentGroup id="background_input">
+                <include segmentGroup="basal1"/>
+            </segmentGroup>
+
+
+        </morphology>
+
+    </cell>
+
+</neuroml>
diff --git a/LEMSexamples/morphologies/pyr_soma_m_in_b_in.cell.nml b/LEMSexamples/morphologies/pyr_soma_m_in_b_in.cell.nml
new file mode 100644
index 0000000..b0561c8
--- /dev/null
+++ b/LEMSexamples/morphologies/pyr_soma_m_in_b_in.cell.nml
@@ -0,0 +1,84 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="pyr_4_sym_soma">
+
+    <include href="Ca_conc.nml"/>
+
+    <include href="Ca_pyr.channel.nml"/>
+
+    <include href="Kahp_pyr.channel.nml"/>
+
+    <include href="Kdr_pyr.channel.nml"/>
+
+    <include href="LeakConductance_pyr.channel.nml"/>
+
+    <include href="Na_pyr.channel.nml"/>
+
+    <cell id="pyr_soma_m_in_b_in">
+
+        <notes>A single segment/compartment cell</notes>
+
+        <morphology id="morphology_pyr_4_sym_soma">
+
+            <segment id="0" name="soma">
+                <proximal x="0.0" y="0.0" z="0.0" diameter="23.0"/>
+                <distal x="0.0" y="17.0" z="0.0" diameter="23.0"/>
+            </segment>
+
+            <segmentGroup id="soma" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="0"/>
+            </segmentGroup>
+
+            <segmentGroup id="all">
+                <include segmentGroup="soma"/>
+            </segmentGroup>
+
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">    <!--Soma group-->
+
+                <include segmentGroup="soma"/>
+            </segmentGroup>
+
+            
+        </morphology>
+
+            <!--Adding the biophysical parameters-->
+
+        <biophysicalProperties id="biophys">
+
+            <membraneProperties>
+                
+                <channelDensity condDensity="10.0 mS_per_cm2" id="Ca_pyr_soma_group" ionChannel="Ca_pyr" segmentGroup="soma_group" ion="ca" erev="80.0 mV"/>
+                
+                <channelDensity condDensity="2.5 mS_per_cm2" id="Kahp_pyr_soma_group" ionChannel="Kahp_pyr" segmentGroup="soma_group" ion="k" erev="-75.0 mV"/>
+                
+                <channelDensity condDensity="80.0 mS_per_cm2" id="Kdr_pyr_soma_group" ionChannel="Kdr_pyr" segmentGroup="soma_group" ion="k" erev="-75.0 mV"/>
+                
+                <channelDensity condDensity="0.1420051 mS_per_cm2" id="LeakConductance_pyr_all" ionChannel="LeakConductance_pyr" erev="-66.0 mV" ion="non_specific"/>
+                
+                <channelDensity condDensity="120.0 mS_per_cm2" id="Na_pyr_soma_group" ionChannel="Na_pyr" segmentGroup="soma_group" ion="na" erev="55.0 mV"/>
+                
+
+                <spikeThresh value="0.0 mV"/>
+
+                <specificCapacitance value="2.84 uF_per_cm2"/>
+
+                <initMembPotential value="-65.0 mV"/>
+
+            </membraneProperties>
+
+            <intracellularProperties>
+
+                <species id="ca" ion="ca" concentrationModel="Ca_conc" initialConcentration="5.0E-11 mol_per_cm3" initialExtConcentration="3.0E-6 mol_per_cm3"/>
+
+                <resistivity value="0.2 kohm_cm"/>
+
+            </intracellularProperties>
+
+        </biophysicalProperties>
+
+    </cell>
+    
+</neuroml>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/pyr_soma_m_in_b_out.cell.nml b/LEMSexamples/morphologies/pyr_soma_m_in_b_out.cell.nml
new file mode 100644
index 0000000..7b11f33
--- /dev/null
+++ b/LEMSexamples/morphologies/pyr_soma_m_in_b_out.cell.nml
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="pyr_4_sym_soma">
+
+    <include href="pyr_biophysics.nml"/>
+
+    <cell id="pyr_soma_m_in_b_out" biophysicalProperties="biophys">
+
+        <notes>A single segment/compartment cell</notes>
+
+        <morphology id="morphology_pyr_4_sym_soma">
+
+            <segment id="0" name="soma">
+                <proximal x="0.0" y="0.0" z="0.0" diameter="23.0"/>
+                <distal x="0.0" y="17.0" z="0.0" diameter="23.0"/>
+            </segment>
+
+            <segmentGroup id="soma" neuroLexId="sao864921383">    <!--
+                This group contains an unbranched set of segments, and all of the segmentGroups marked with
+                neuroLexId = sao864921383 form a non-overlapping set of all of the segments. 
+                These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
+
+                <member segment="0"/>
+            </segmentGroup>
+
+            <segmentGroup id="all">
+                <include segmentGroup="soma"/>
+            </segmentGroup>
+
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">    <!--Soma group-->
+
+                <include segmentGroup="soma"/>
+            </segmentGroup>
+
+            
+        </morphology>
+
+    </cell>
+    
+</neuroml>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/pyr_soma_m_out_b_in.cell.nml b/LEMSexamples/morphologies/pyr_soma_m_out_b_in.cell.nml
new file mode 100644
index 0000000..8aa95c4
--- /dev/null
+++ b/LEMSexamples/morphologies/pyr_soma_m_out_b_in.cell.nml
@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="pyr_4_sym_soma">
+
+    <include href="Ca_conc.nml"/>
+
+    <include href="Ca_pyr.channel.nml"/>
+
+    <include href="Kahp_pyr.channel.nml"/>
+
+    <include href="Kdr_pyr.channel.nml"/>
+
+    <include href="LeakConductance_pyr.channel.nml"/>
+
+    <include href="Na_pyr.channel.nml"/>
+
+    <include href="pyr_4_sym_soma_morph.nml"/>
+
+    <cell id="pyr_soma_m_out_b_in" morphology="morphology_pyr_soma">
+
+        <notes>A single segment/compartment cell</notes>
+
+
+            <!--Adding the biophysical parameters-->
+
+        <biophysicalProperties id="biophys">
+
+            <membraneProperties>
+                
+                <channelDensity condDensity="10.0 mS_per_cm2" id="Ca_pyr_soma_group" ionChannel="Ca_pyr" segmentGroup="soma_group" ion="ca" erev="80.0 mV"/>
+                
+                <channelDensity condDensity="2.5 mS_per_cm2" id="Kahp_pyr_soma_group" ionChannel="Kahp_pyr" segmentGroup="soma_group" ion="k" erev="-75.0 mV"/>
+                
+                <channelDensity condDensity="80.0 mS_per_cm2" id="Kdr_pyr_soma_group" ionChannel="Kdr_pyr" segmentGroup="soma_group" ion="k" erev="-75.0 mV"/>
+                
+                <channelDensity condDensity="0.1420051 mS_per_cm2" id="LeakConductance_pyr_all" ionChannel="LeakConductance_pyr" erev="-66.0 mV" ion="non_specific"/>
+                
+                <channelDensity condDensity="120.0 mS_per_cm2" id="Na_pyr_soma_group" ionChannel="Na_pyr" segmentGroup="soma_group" ion="na" erev="55.0 mV"/>
+                
+
+                <spikeThresh value="0.0 mV"/>
+
+                <specificCapacitance value="2.84 uF_per_cm2"/>
+
+                <initMembPotential value="-65.0 mV"/>
+
+            </membraneProperties>
+
+            <intracellularProperties>
+
+                <species id="ca" ion="ca" concentrationModel="Ca_conc" initialConcentration="5.0E-11 mol_per_cm3" initialExtConcentration="3.0E-6 mol_per_cm3"/>
+
+                <resistivity value="0.2 kohm_cm"/>
+
+            </intracellularProperties>
+
+        </biophysicalProperties>
+
+    </cell>
+    
+</neuroml>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/pyr_soma_m_out_b_out.cell.nml b/LEMSexamples/morphologies/pyr_soma_m_out_b_out.cell.nml
new file mode 100644
index 0000000..506ef23
--- /dev/null
+++ b/LEMSexamples/morphologies/pyr_soma_m_out_b_out.cell.nml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="pyr_4_sym_soma">
+
+    <include href="pyr_4_sym_soma_morph.nml"/>
+    <include href="pyr_biophysics.nml"/>
+
+    <cell id="pyr_soma_m_out_b_out" morphology="morphology_pyr_soma" biophysicalProperties="biophys">
+
+        <notes>A single segment/compartment cell</notes>
+
+    </cell>
+    
+</neuroml>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/pyrfull_in.net.nml b/LEMSexamples/morphologies/pyrfull_in.net.nml
new file mode 100644
index 0000000..6abb92c
--- /dev/null
+++ b/LEMSexamples/morphologies/pyrfull_in.net.nml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="pyr_4_sym_soma">
+
+    <include href="pyr_4_sym.cell.nml"/>
+
+    <pulseGenerator id="Input_3" delay="100.0ms" duration="500.0ms" amplitude="2.0E-4uA"/>
+
+    <network id="network" type="networkWithTemperature" temperature="6.3 degC">
+
+        <population id="pyramidals" component="pyr_4_sym" type="populationList" size="1">
+           <annotation>
+                <property tag="color" value="0.7421875 0.07421875 0.95703125"/>
+            </annotation>
+            <instance id="0">
+                <location x="400.0" y="0.0" z="0.0"/>
+            </instance>
+        </population>
+
+        <inputList id="Input_3" component="Input_3" population="pyramidals">
+            <input id="0" target="../pyramidals/0/pyr_4_sym" destination="synapses"/>
+        </inputList>
+
+
+    </network>
+    
+</neuroml>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/pyrfull_out.net.nml b/LEMSexamples/morphologies/pyrfull_out.net.nml
new file mode 100644
index 0000000..d994109
--- /dev/null
+++ b/LEMSexamples/morphologies/pyrfull_out.net.nml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="pyr_4_sym_soma">
+
+    <include href="pyr_full_out.cell.nml"/>
+
+    <pulseGenerator id="Input_3" delay="100.0ms" duration="500.0ms" amplitude="2.0E-4uA"/>
+
+    <network id="network" type="networkWithTemperature" temperature="6.3 degC">
+
+        <population id="pyramidals" component="pyr_full_out" type="populationList" size="1">
+           <annotation>
+                <property tag="color" value="0.7421875 0.07421875 0.95703125"/>
+            </annotation>
+            <instance id="0">
+                <location x="400.0" y="0.0" z="0.0"/>
+            </instance>
+        </population>
+
+        <inputList id="Input_3" component="Input_3" population="pyramidals">
+            <input id="0" target="../pyramidals/0/pyr_full_out" destination="synapses"/>
+        </inputList>
+
+
+    </network>
+    
+</neuroml>
\ No newline at end of file
diff --git a/LEMSexamples/morphologies/test_all.sh b/LEMSexamples/morphologies/test_all.sh
new file mode 100755
index 0000000..c35aa7e
--- /dev/null
+++ b/LEMSexamples/morphologies/test_all.sh
@@ -0,0 +1,29 @@
+#!/bin/bash
+set -ex
+
+pynml -validate C*nml *cell.nml *channel.nml 
+
+pynml-summary pyr_soma_m_in_b_in.cell.nml -v
+pynml-summary pyr_soma_m_in_b_out.cell.nml -v
+pynml-summary pyr_soma_m_out_b_in.cell.nml -v
+pynml-summary pyr_soma_m_out_b_out.cell.nml -v
+
+pynml LEMS_m_in_b_in.xml -nogui
+
+pynml LEMS_m_in_b_in.xml -neuron -run -nogui
+pynml LEMS_m_in_b_out.xml -neuron -run -nogui
+pynml LEMS_m_out_b_in.xml -neuron -run -nogui
+pynml LEMS_m_out_b_out.xml -neuron -run -nogui
+
+pynml LEMS_m_in_b_in.xml -netpyne -run
+pynml LEMS_m_in_b_out.xml -netpyne -run
+pynml LEMS_m_out_b_in.xml -netpyne -run
+pynml LEMS_m_out_b_out.xml -netpyne -run
+
+pynml LEMS_pyrfull_in.xml -neuron -run -nogui
+pynml LEMS_pyrfull_in.xml -netpyne -run
+
+pynml LEMS_pyrfull_out.xml -neuron -run -nogui
+pynml LEMS_pyrfull_out.xml -netpyne  -run 
+
+echo "All tests completed!"