cnstellate is a NEURON package simulating the cochlear nucleus stellate microcircuit as part of my PhD.

Citation: Eager, M. A., The stellate microcircuit of the cochlear nucleus: design and optimisation of a biophysically-realistic neural network model, PhD thesis, The University of Melbourne, 2013.

GPLv3 Licence Copyright 2013 Michael Eager (mick.eager@gmail.com).

The cnstellate software is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. The cnstellate software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with the cnstellate source code. If not, see http://www.gnu.org/licenses/.

I generally setup two versions of NEURON one for testing with a GUI and the other with MPI. PVM may also be used to generate parallel simulations, but mpich2 or open-mpi is preferred.

The up to date NEURON package can be pulled from the NEURON mercurial repository (http://www.neuron.yale.edu/hg/neuron/iv and http://www.neuron.yale.edu/hg/neuron/nrn) Each of the source packages need to run some autotools scripts in ./build.sh in their directories.

cd ~
mkdir -p src/neuron
cd src/neuron
hg clone http://www.neuron.yale.edu/hg/neuron/iv
hg clone http://www.neuron.yale.edu/hg/neuron/nrn
cd iv
./build.sh
cd ../nrn
./build.sh

Default installation (/usr/local) requires root privileges. I prefer to install IV into its source directory.

cd ~/src/neuron/iv
./configure --prefix=`pwd` 
make && make install

Now make separate builds for the gui

cd ~/src/neuron
mkdir nrngui
cd nrngui
../configure --prefix=`pwd` --with-iv=$HOME/src/neuron/iv --without-paranrn
nice make -j3 && make install

and for the MPI version

cd ..
mkdir mpi
../configure --prefix=`pwd` --without-iv --with-paranrn
nice make -j3 && make install

Pull the repository from bitbucket.

hg clone https://bitbucket.org/eagerm/cnstellate

In the working cnstellate directory, setup two linkable libraries against the two nrn builds.

See the Makefile for instructions to make either the gui or mpi version, otherwise use “make all”. This calls the appropriate ‘nrnivmodl’ script to convert the *.mod files to a dynamic library. The compiled files, by default in folder <arch>, are moved to either gui or mpi folders.

make gui

or

make mpi

Uncomment the variables below in an_zilany_v4.mod to enable the ffGn function. The default mode replaces the ffGn function with a constant value related to the spontaneous rate of the ANF.

 /* #define DEBUG   */
 /* #define _FFGN_  */

To run a script in gui mode using the DS cell rate level optimisation routine:

 ./gui/special DS_RateLevel.hoc -

The dash on the end allows the user to enter the interactive mode after loading the HOC file.

To run the script and automatically start the optimsation routine for each of the cell types in the microcircuit.

Golgi cells were fit to monotonic rate level responses in the marginal shell (Ghoshal and Kim 1998)

./gui/special golgi_RateLevel.hoc -c "run_optimisation()"

Timing of GABAergic inputs to DS cells (from golgi cells) was fit using click-pair recovery times.

./gui/special DS_clickRecovery.hoc -c "run_optimisation()"

D-stellate cell’s input parameters were optimised using data from large multipolar responses with onset chopper PSTH’s (Arnott et al 2003).

./gui/special DS_RateLevel.hoc -c "run_optimisation()"

Tuberculoventral cell model’s rate-level responses are optimised to Type-II units in the DCN (Spirou et al 1999).

./gui/special TV_RateLevel.hoc -c "run_optimisation()"

For the T-stellate cells, optimisation for three chopper subtypes are included (CS,CT1 and CT2) based on average intracellular responses (Paolini, Needham, et al. 2004,2005)

./mpi/special TStellate2.hoc -c "optimise_CS()"
./mpi/special TStellate2.hoc -c "optimise_CT1()"
./mpi/special TStellate2.hoc -c "optimise_CT2()"

Chapters 3 and 4 simulate the full CNSM model to tones, noise and AM stimuli. To run all the verification stimuli and AM stimuli on the CNSM model using the second ChT TS cell model parameters, use:

./mpi/special AMResponses.hoc -c "SimpleResponses_CT2()" -c "AMresponse_CT2()"

ResponseRoutines.hoc includes the methods to simulate various battery tests for auditory neurons.

• RateLevelFunction() short tone bursts at fixed frequency and incrementing intensity
• NoiseRateLevelFunction() short noise bursts with incrementing intensity
• MaskedRateLevelFunction() short tone+ noise bursts, fixed noise at intensity with 50% rate in NRL, tone with fixed frequency and incrementing intensity
• MaskedResponseCurve() masking noise at fixed intensity plus short tone bursts at fixed frequency and increasing intensity
• ResponseArea() short tone bursts: 2D map of frequency and intensity restricted to the receptive field of the unit
• F0_Response() long AM tones at fixed carrier and modulation frequencies, with short increments in intensity
• ModulationTransferFunction() long duration, sinusoidal amplitude modulation stimuli at fixed carrier frequency. Modulation frequency ranges from 50 to 1200 Hz. Stimulus intensity was varied from 20 to 80 dB SPL in 20 dB steps.

The output of these methods is saved in subdirectories depending on the method name and in an ordered arrangement of independent variables.

For example, the ModulationTransferFunction() outputs to: <fileroot>\/ModulationTransferFunction\/<intensity SPL>\/<modulation frequency>\/

The contents of a MTF simulation

$ ls TStellate2_CS/ModulationTransferFunction/80/100
an.HSR.hist       psth.2.dat       spctFULL.1.dat  vs.1.dat
anHSR_raster.dat  psth.3.dat       spctFULL.2.dat  vs.2.dat
anLSR_raster.dat  rateplace.0.dat  spctFULL.3.dat  vs.3.dat
ds_raster.dat     rateplace.1.dat  spctFULL.4.dat  vs.4.dat
glg_raster.dat    rateplace.2.dat  spctFULL.5.dat  vs.5.dat
periodhist.0.dat  rateplace.3.dat  spctVS.0.dat    vsSPIKES.0.dat
periodhist.1.dat  smhist.dat       spctVS.1.dat    vsSPIKES.1.dat
periodhist.2.dat  spct.0.dat       spctVS.2.dat    vsSPIKES.2.dat
periodhist.3.dat  spct.1.dat       spctVS.3.dat    vsSPIKES.3.dat
periodhist.4.dat  spct.2.dat       spctVS.4.dat    vsSPIKES.4.dat
periodhist.5.dat  spct.3.dat       spctVS.5.dat    vsSPIKES.5.dat
pow.dat           spct.4.dat       ts_raster.dat
psth.0.dat        spct.5.dat       tv_raster.dat
psth.1.dat        spctFULL.0.dat   vs.0.dat

• rateplace.*.dat: mean firing rate from t_start to t_stop (ms)
• vs.*.dat: period histogram method (default calcisi.hoc)
• vsSPIKES.*.dat: raw spike method with spikes from t_start+10 to t_stop (ms)

To run cnstellate in non-gui mode, use the mpi version. When the MPI version is run without mpiexec or mpirun, the program run identical to the gui version without any visual windows.

 ./mpi/special DS_RateLevel.hoc -

For parallel cnstellate to work, the MPI version should be run in the background from the mpispecial script or in batch mode:

./mpispecial np par_batch.hoc > /tmp/batch.log 2>&1 &

np is the number of processors requested. See mpispecial for how the parallel mode is implemented.

To run a test on different numbers of processors, see the example script test1.sh or run it using

./test1.sh

Submit the script to a PBS engine using

qsub -q medium.q -b y -V -cwd `pwd`/mpispecial 5 par_batch.hoc