# ankursinha.in/blog

neuroscience/fedora/musings

Fri 02 September 2016

# Using NEURON - Part II

Posted by ankur in Research (328 words, approximately a 2 minute read)

ModelDB is a popular resource where the computational neuroscience community puts up models that were used in various publications. Since I'm quite new to NEURON, I thought I'd play with some existing models to get a hang of things. Here I document how to run an existing model.

ModelDB has quite a few models that use NEURON. Find one that suits you. I'll pick L5b PC model constrained for BAC firing and perisomatic current step firing (Hay et al., 2011) for now.

## Download the model

Download the zip file from the model page to a convenient location. There's a link right on the top of the page. Extract it.

$unzip L5bPCmodelsEH.zip$ lash
total 668K
4.0K drwxr-xr-x. 7 asinha asinha 4.0K Mar 30  2013 L5bPCmodelsEH
664K -rw-r-----. 1 asinha asinha 662K Sep  2 13:55 L5bPCmodelsEH.zip


## Building and running the model

Enter the directory:

cd L5bPCmodelsEH/


NEURON code comprises of two sets of code files. You have the HOC files, and the NMODL files. NMODL files need to be compiled before the model can be run.

$~/dump/neuron-installation/x86_64/bin/nrnivmodl mod Creating x86_64 directory for .o files. /home/asinha/dump/neuron-blog/L5bPCmodelsEH mod/CaDynamics_E2.mod mod/Ca_HVA.mod mod/Ca_LVAst.mod mod/epsp.mod mod/Ih.mod mod/Im.mod mod/K_Pst.mod mod/K_Tst.mod mod/Nap_Et2.mod mod/NaTa_t.mod mod/NaTs2_t.mod mod/SK_E2.mod mod/SKv3_1.mod CaDynamics_E2.mod Ca_HVA.mod Ca_LVAst.mod epsp.mod Ih.mod Im.mod K_Pst.mod K_Tst.mod Nap_Et2.mod NaTa_t.mod NaTs2_t.mod SK_E2.mod SKv3_1.mod "/home/asinha/dump/neuron-installation/x86_64/bin/nocmodl" CaDynamics_E2 Translating CaDynamics_E2.mod into CaDynamics_E2.c Thread Safe "/home/asinha/dump/neuron-installation/share/nrn/libtool" --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I.. -I"/home/asinha/dump/neuron-installation/include/nrn" -I"/home/asinha/dump/neuron-installation/x86_64/lib" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c -o CaDynamics_E2.lo CaDynamics_E2.c libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I.. -I/home/asinha/dump/neuron-installation/include/nrn -I/home/asinha/dump/neuron-installation/x86_64/lib -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c CaDynamics_E2.c -fPIC -DPIC -o .libs/CaDynamics_E2.o CaDynamics_E2.c:94:34: warning: missing braces around initializer [-Wmissing-braces] static VoidFunc hoc_intfunc[] = { ... .... ... ...  You'll see a new x86_64 directory which contains the compiled code. Now, simply run NEURON as usual. If everything went well, the simulation will run: $ ~/dump/neuron-installation/x86_64/bin/nrngui mosinit.hoc


Remember that you must run nrngui in the directory where the x86_64 directory resides for NEURON to find it.

That's it!