Downloaded latest zips from NMC & extracted here

Author: pgleeson

NMC/parser/L1_HAC_cNAC187_1/CHANGELOG

@@ -1,3 +1,4 @@
+1.0.11: Made compatible with python3. Improved README
 1.0.10: Increased the current to calculate the Rin to get above the noise level
         for models with stochastic channels
 1.0.9:  Every model package now contains a cellinfo.json file with e.g. the

NMC/parser/L1_HAC_cNAC187_1/README

@@ -6,8 +6,8 @@ ModelDB (http://senselab.med.yale.edu/ModelDB/). They assume you have installed
 a recent NEURON package (>7.3 is known to work), available at
 http://www.neuron.yale.edu.
 
-Linux / Unix
-------------
+Linux / Unix / Mac
+------------------
 1. Download one of the model packages from the Downloads section, or from an
 me-type fact sheet.  For this example we will download the package named
 L5_DBC_cACint209_3.zip (i.e. m-type L5_DBC, e-type cAC, exemplar 3)
@@ -23,12 +23,6 @@ user@machine:~/dev/sim/neuron/L5_DBC_cACint209_3$ sh run_hoc.sh
 
 4. Read the 'How to use the ME-type model GUI' section below
 
-If you have installed Neuron with Python support, you can run a python version
-of the model. This script will run without a GUI, and will produce traces for
-step current 1, 2 and 3 in the directory python_recordings
-
-user@machine:~/dev/sim/neuron/L5_DBC_cACint209_3$ sh run_py.sh
-
 Windows
 -------
 1. Download one of the model packages from the Downloads section, or from an
@@ -47,33 +41,24 @@ unzipped cell package directory
 5. The GUI should load automatically. Read the 'How to use the ME-type model
 GUI' section below
 
-Mac OS X
---------
-1. Download one of the model packages from the Downloads section, or from an
-me-type fact sheet.  For this example we will download the package named
-L5_DBC_cACint209_3.zip
-
-2. Unzip the downloaded package
-
-3. Drag the 'mechanisms' directory inside the unzipped cell package directory
-onto the mknrndll.app icon
+Running the Python version of the model package on Linux / Unix / Mac OS X
+==========================================================================
+Both Python 2.6+ as 3.4+ are supported.
+If you have installed Neuron with Python support, you can run a python version
+of the model. The python script depends on numpy and matplotlib, so first 
+install these packages with e.g. 'pip install numpy matplotlib'
+The script will run without a GUI, and will produce traces for
+step current 1, 2 and 3 in the directory python_recordings
 
-4. Run nrngui.app. Point the 'File->load dll' menu option to
-mechanisms/x86_64/.libs/libnrnmech.so (You probably need to change the Filter
-from *.dll to *.so. Depending on your computer's processor type x86_64 might
-also be e.g. i686). Using 'File->load hoc' load the mosinit.hoc file in the
-root directory of the cell package directory.
+user@machine:~/dev/sim/neuron/L5_DBC_cACint209_3$ sh run_py.sh
 
-5. The GUI should load automatically.. Read the 'How to use the ME-type model
-GUI' section below How to use the ME-type model GUI
+How to use the ME-type model GUI
+================================
 
 To start simulating the model, press the Init & Run button. Initially there are
 no stimuli present, which means that the cell will stay at its resting membrane
 potential.
 
-How to use the ME-type model GUI
-================================
-
 There are three panels that show the output of the model. One is a graph with
 the membrane voltage recorded in the soma (units: ms and mV), the two other
 panels have a representation of the cell's morphology. The sections in the
@@ -96,3 +81,39 @@ represented by a Poisson spike train, and the synapses will receive input from
 these virtual cell. The default firing rate of these virtual cells is set to 10
 Hz. The user can change these value by changing the input field next to the
 respective m-type activation button.
+
+Installing Neuron on Mac OS X using Homebrew
+============================================
+
+In our experience the Homebrew package manager is the most convenient way to 
+get a commandline version of Neuron that has both X11 and Python support 
+running on your Mac.
+
+1. Install Homebrew by following the instruction on http://brew.sh, or:
+
+ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)")
+
+2. Tap the Science Homebrew repo from 
+
+https://github.com/Homebrew/homebrew-science 
+
+by executing:
+
+brew tap homebrew/science
+
+3. Now you can install Neuron:
+
+brew install neuron
+
+This will install all the necessary software dependencies 
+like InterViews, X11, ...
+
+You can test the installation by executing:
+
+nrngui
+
+which should start the Neuron GUI
+
+To test the Neuron python module:
+
+python -c 'import neuron'

NMC/parser/L1_HAC_cNAC187_1/VERSION

@@ -1,2 +1,2 @@
-1.0.10
-2015/07/20
+1.0.11
+2015/10/07

NMC/parser/L1_HAC_cNAC187_1/run.py

@@ -52,7 +52,7 @@ def create_cell(add_synapses=True):
 
     # Instantiate the cell from the template
 
-    print "Loading cell cNAC187_L1_HAC_f8c9772d9d"
+    print("Loading cell cNAC187_L1_HAC_f8c9772d9d")
     cell = neuron.h.cNAC187_L1_HAC_f8c9772d9d(1 if add_synapses else 0)
     return cell
 
@@ -132,7 +132,12 @@ def run_step(step_number, plot_traces=None):
     soma_voltage_filename = os.path.join(
         recordings_dir,
         'soma_voltage_step%d.dat' % step_number)
-    numpy.savetxt(soma_voltage_filename, zip(time, soma_voltage))
+    numpy.savetxt(
+            soma_voltage_filename,
+            numpy.transpose(
+               numpy.vstack((
+                    time,
+                    soma_voltage))))
 
     print('Soma voltage for step %d saved to: %s'
           % (step_number, soma_voltage_filename))

NMC/parser/L1_HAC_cNAC187_1/run_py.sh

@@ -1,2 +1,7 @@
 nrnivmodl ./mechanisms
-./run.py "$@"
+
+# Use for python 2.6+
+python ./run.py "$@"
+
+# Use for python 3.4+
+# python3 ./run.py "$@"

NMC/parser/L23_LBC_cSTUT189_1/CHANGELOG

@@ -1,3 +1,4 @@
+1.0.11: Made compatible with python3. Improved README
 1.0.10: Increased the current to calculate the Rin to get above the noise level
         for models with stochastic channels
 1.0.9:  Every model package now contains a cellinfo.json file with e.g. the

NMC/parser/L23_LBC_cSTUT189_1/README

@@ -6,8 +6,8 @@ ModelDB (http://senselab.med.yale.edu/ModelDB/). They assume you have installed
 a recent NEURON package (>7.3 is known to work), available at
 http://www.neuron.yale.edu.
 
-Linux / Unix
-------------
+Linux / Unix / Mac
+------------------
 1. Download one of the model packages from the Downloads section, or from an
 me-type fact sheet.  For this example we will download the package named
 L5_DBC_cACint209_3.zip (i.e. m-type L5_DBC, e-type cAC, exemplar 3)
@@ -23,12 +23,6 @@ user@machine:~/dev/sim/neuron/L5_DBC_cACint209_3$ sh run_hoc.sh
 
 4. Read the 'How to use the ME-type model GUI' section below
 
-If you have installed Neuron with Python support, you can run a python version
-of the model. This script will run without a GUI, and will produce traces for
-step current 1, 2 and 3 in the directory python_recordings
-
-user@machine:~/dev/sim/neuron/L5_DBC_cACint209_3$ sh run_py.sh
-
 Windows
 -------
 1. Download one of the model packages from the Downloads section, or from an
@@ -47,33 +41,24 @@ unzipped cell package directory
 5. The GUI should load automatically. Read the 'How to use the ME-type model
 GUI' section below
 
-Mac OS X
---------
-1. Download one of the model packages from the Downloads section, or from an
-me-type fact sheet.  For this example we will download the package named
-L5_DBC_cACint209_3.zip
-
-2. Unzip the downloaded package
-
-3. Drag the 'mechanisms' directory inside the unzipped cell package directory
-onto the mknrndll.app icon
+Running the Python version of the model package on Linux / Unix / Mac OS X
+==========================================================================
+Both Python 2.6+ as 3.4+ are supported.
+If you have installed Neuron with Python support, you can run a python version
+of the model. The python script depends on numpy and matplotlib, so first 
+install these packages with e.g. 'pip install numpy matplotlib'
+The script will run without a GUI, and will produce traces for
+step current 1, 2 and 3 in the directory python_recordings
 
-4. Run nrngui.app. Point the 'File->load dll' menu option to
-mechanisms/x86_64/.libs/libnrnmech.so (You probably need to change the Filter
-from *.dll to *.so. Depending on your computer's processor type x86_64 might
-also be e.g. i686). Using 'File->load hoc' load the mosinit.hoc file in the
-root directory of the cell package directory.
+user@machine:~/dev/sim/neuron/L5_DBC_cACint209_3$ sh run_py.sh
 
-5. The GUI should load automatically.. Read the 'How to use the ME-type model
-GUI' section below How to use the ME-type model GUI
+How to use the ME-type model GUI
+================================
 
 To start simulating the model, press the Init & Run button. Initially there are
 no stimuli present, which means that the cell will stay at its resting membrane
 potential.
 
-How to use the ME-type model GUI
-================================
-
 There are three panels that show the output of the model. One is a graph with
 the membrane voltage recorded in the soma (units: ms and mV), the two other
 panels have a representation of the cell's morphology. The sections in the
@@ -96,3 +81,39 @@ represented by a Poisson spike train, and the synapses will receive input from
 these virtual cell. The default firing rate of these virtual cells is set to 10
 Hz. The user can change these value by changing the input field next to the
 respective m-type activation button.
+
+Installing Neuron on Mac OS X using Homebrew
+============================================
+
+In our experience the Homebrew package manager is the most convenient way to 
+get a commandline version of Neuron that has both X11 and Python support 
+running on your Mac.
+
+1. Install Homebrew by following the instruction on http://brew.sh, or:
+
+ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)")
+
+2. Tap the Science Homebrew repo from 
+
+https://github.com/Homebrew/homebrew-science 
+
+by executing:
+
+brew tap homebrew/science
+
+3. Now you can install Neuron:
+
+brew install neuron
+
+This will install all the necessary software dependencies 
+like InterViews, X11, ...
+
+You can test the installation by executing:
+
+nrngui
+
+which should start the Neuron GUI
+
+To test the Neuron python module:
+
+python -c 'import neuron'

NMC/parser/L23_LBC_cSTUT189_1/VERSION

@@ -1,2 +1,2 @@
-1.0.10
-2015/07/20
+1.0.11
+2015/10/07

NMC/parser/L23_LBC_cSTUT189_1/run.py

@@ -52,7 +52,7 @@ def create_cell(add_synapses=True):
 
     # Instantiate the cell from the template
 
-    print "Loading cell cSTUT189_L23_LBC_e6e8f83407"
+    print("Loading cell cSTUT189_L23_LBC_e6e8f83407")
     cell = neuron.h.cSTUT189_L23_LBC_e6e8f83407(1 if add_synapses else 0)
     return cell
 
@@ -132,7 +132,12 @@ def run_step(step_number, plot_traces=None):
     soma_voltage_filename = os.path.join(
         recordings_dir,
         'soma_voltage_step%d.dat' % step_number)
-    numpy.savetxt(soma_voltage_filename, zip(time, soma_voltage))
+    numpy.savetxt(
+            soma_voltage_filename,
+            numpy.transpose(
+               numpy.vstack((
+                    time,
+                    soma_voltage))))
 
     print('Soma voltage for step %d saved to: %s'
           % (step_number, soma_voltage_filename))

NMC/parser/L23_LBC_cSTUT189_1/run_py.sh

@@ -1,2 +1,7 @@
 nrnivmodl ./mechanisms
-./run.py "$@"
+
+# Use for python 2.6+
+python ./run.py "$@"
+
+# Use for python 3.4+
+# python3 ./run.py "$@"