Running Models from ModelDB

Post Reply
jtchang
Posts: 1
Joined: Wed Sep 24, 2014 10:37 am

Running Models from ModelDB

Post by jtchang » Thu Sep 25, 2014 12:43 pm

Hi, I'm new to NEURON and I tried running one of the models from ModelDB. Specifically, I'm trying to run the Spinal Motor Neuron (McIntyre et al 2002). I've installed NEURON and downloaded the zip file for this model.

I've tried running the model by double clicking mosinit.hoc. I get this error message:

Code: Select all

NEURON -- VERSION 7.3 ansi (1078:2b0c984183df) 2014-04-04
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2014
See http://www.neuron.yale.edu/neuron/credits

        1
        1
nrniv: syntax error
 in MRGaxon.hoc near line 80
                        insert axnode
                ^
        xopen("MRGaxon.hoc")
oc>
When I tried running MRGaxon.hoc, I get this instead:

Code: Select all

NEURON -- VERSION 7.3 ansi (1078:2b0c984183df) 2014-04-04
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2014
See http://www.neuron.yale.edu/neuron/credits

cygwin warning:
  MS-DOS style path detected: \Program Files (x86)\OpenLibraries\python
  Preferred POSIX equivalent is: /cygdrive/c/Program Files (x86)/OpenLibraries/p                            ython
  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
: not foundd.sh: 2: /lib/hocload.sh:
: not foundd.sh: 5: /lib/hocload.sh:
: not foundd.sh: 8: /lib/hocload.sh:
/lib/hocload.sh: 24: /lib/hocload.sh: Syntax error: word unexpected (expecting "                            do")
nrniv: can't run: $NEURONHOME/lib/hocload.sh proc nrnmainmenu 1
 in MRGaxon.hoc near line 18
 load_proc("nrnmainmenu")
                         ^
        load_proc("nrnmainmenu")
oc>
I'm probably doing something wrong, but I'm not sure what. Are there environment variables that I need to have? Am I putting the files in the wrong folder?

Thank you very much for your help!

ted
Site Admin
Posts: 5057
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Running Models from ModelDB

Post by ted » Thu Sep 25, 2014 10:20 pm

This rather cryptic error message

Code: Select all

nrniv: syntax error
in MRGaxon.hoc near line 80
                        insert axnode
                ^
        xopen("MRGaxon.hoc")
is the clue. It means that you need to compile the NMODL ("mod") files that are packaged with the model's hoc and ses files. For a short description of how to do this, click on the link
Help downloading and running models
which is in that row of buttons that includes the "Download zip file" button on the main page of the model's entry.

You might find it helpful to poke around NEURON's Documentation page http://www.neuron.yale.edu/neuron/docs for other information.

Post Reply