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Course: Using ModelDB Mainen and Sejnowski 1996

Posted: Fri Sep 03, 2010 3:58 pm
by nianwosuh
I am working throug the on-line course material: Using ModelDB, the second example, the paper by Mainen and Sejinowski, 1995. I compiled the mod file in the patdemo folder and tried to run the mosinit.hoc. It generated an error message :
syntax error
in demofig1.hoc near line 197
forall insert na
^
I located this line in the demofig1.hoc, but not sure what the "insert na" was supposed to be.

Please do you have any idea what the orignal authors intended the "insert na" to be?

Thank you
Irene

Re: Course: Using ModelDB Mainen and Sejnowski 1996

Posted: Fri Sep 03, 2010 8:24 pm
by neuromau
The Mainen and Sejinowski, 1996 model has an Na (sodium channel) mechanism, as you can see from looking at the files in that modeldb entry (there is a file called "na.mod"). So that line is for inserting the sodium channel mechanism defined in "na.mod" into all the sections.

Re: Course: Using ModelDB Mainen and Sejnowski 1996

Posted: Sat Sep 04, 2010 12:53 pm
by ted
nianwosuh wrote:I am working throug the on-line course material: Using ModelDB, the second example, the paper by Mainen and Sejinowski, 1995.
That's Mainen & Sejnowski 1996.
I compiled the mod file in the patdemo folder and tried to run the mosinit.hoc. It generated an error message
When NEURON first starts, it prints out a few lines that tell its version number, and then it prints out the names of any mod files whose compiled mechanisms it has loaded.

NEURON should report the following, for this particular model:

Code: Select all

Additional mechanisms from files
 cad.mod ca.mod kca.mod km.mod kv.mod na.mod
Did you see such a message, and if so, exactly what did it say?

Re: Course: Using ModelDB Mainen and Sejnowski 1996

Posted: Tue Sep 07, 2010 12:40 pm
by nianwosuh
When I run the mosint.hoc, this is the additional mechanisms it has: Additional mechanisms from files
ca.mod cad.mod kca.mod km.mod kv.mod na.mod.

Thank you
Irene

Re: Course: Using ModelDB Mainen and Sejnowski 1996

Posted: Tue Sep 07, 2010 2:10 pm
by ted
nianwosuh wrote:When I run the mosint.hoc, this is the additional mechanisms it has: Additional mechanisms from files
ca.mod cad.mod kca.mod km.mod kv.mod na.mod.
Then the mod files compiled successfully, and NEURON is loading the mechanisms when it starts up. So the Mainen & Sejnowski model should not have any problems. Were you writing some code of your own?

Re: Course: Using ModelDB Mainen and Sejnowski 1996

Posted: Wed Sep 08, 2010 4:43 pm
by nianwosuh
I did not write any code. I simply followed every instruction.

I have recompiled the mod and restarted NEURON and there was no problem.

Thank you

Re: Course: Using ModelDB Mainen and Sejnowski 1996

Posted: Wed Sep 08, 2010 6:51 pm
by ted
Well, sounds like the first compilation didn't work properly for some reason or other.