Cant run a program given by my supervisor

[firejohnx]

Hey guys,

I am new to NEURON
and I have two problems
1 is my supervisor has given me a program which i cant run on my comp
but it runs ok at his lab
hes using WinXP
and mine is 7
when I run the mosintsimple (which i assume to be the already compiled program starter)
it gives me this error

nrniv: Couldn't find: current.hoc
in /cygdrive/C/Users/John/Desktop/RGC_model/mosinitSimple.hoc near line 2
load_file("current.hoc")

so what is problem there?

and the second question is
my supervisor wants me to input different conductance
one is excitatory and the other is inhibitory
and there are many different values that he wants me to have a combination of these to see the effects
so the best way is to run a for loop
the thing is I dont know how to get inputs from a txt file
I read the tutorial and tried it but its not working
I got the sine wave data from the igor wave generator
which i want to insert to the neuron and run few times to get the action potential numbers average
and i cant now

really appreciate the help

thanks

[ted]

nrniv: Couldn't find: current.hoc
in /cygdrive/C/Users/John/Desktop/RGC_model/mosinitSimple.hoc near line 2
load_file("current.hoc")

so what is problem there?

The MSWin installation of NEURON runs under Cygwin. Cygwin reports paths as if the root directory is called /cygdrive. To discover the MSWin equivalent of a Cygwin path, replace the /cygdrive/C part with C:, and replace all of the forward slashes / with backward slashes.
So the error message tells you three things:
1. there is a file called
mosinitSimple.hoc
in a directory called
C:\Users\John\Desktop\RGC_model
2. the file mosinitSimple.hoc contains the statement
load_file("current.hoc")
3. the statement load_file("current.hoc") fails because there is no file called current.hoc in the same directory as mosinitSimple.hoc

So look in
C:\Users\John\Desktop\RGC_model
and see what's there. Note: case matters. A file called foo.hoc is not the same as a file called Foo.hoc.

and the second question is

First things first. If you can't run the program, you can't do anything else.

[firejohnx]

I am 100% sure that the demo_gfluct.oc is within the same file
but its still not running

[ted]

I am 100% sure that the demo_gfluct.oc is within the same file
but its still not running

demo_gfluct.oc? Who said anything about demo_gfluct.oc?

[firejohnx]

oops
well I opened another one and that one is giving the same problem
(requireing demo_gfluct.oc)
and again the current.hoc is in the same file

[ted]

So you are quite sure that C:\Users\John\Desktop\RGC_model contains a file called current.hoc.

Please do the following:

1. In the NEURON Program Group click on rxvt.sh
This will bring up a window with the name
bash
in the drag bar.

2. In the bash window execute the command
pwd
Tell me what it prints in the bash window (just click and drag to select the output, then use ^v (Control-V) to paste it into your reply on the Forum).

3. Next, execute the command

Code: Select all

cd /cygdrive/C/Users/John/Desktop/RGC_model

4. Now execute
pwd
again, and tell me what it prints in the bash window.

5. Finally, type

Code: Select all

ls

(that's LS in lower case) and tell me what it prints in the bash window.

[firejohnx]

The first result is:
/cygdrive/c

The second one is:
/cygdrive/C/Users/John/Desktop/RGC_model

And the third is:

Code: Select all

Gex.mod        IM.mod                 demo_gfluct.oc  mosinit.hoc
Gex.o          IM.o                   h.mod           mosinitSimple.hoc
Gfluct.mod     INa_traub_shifted.mod  h.o             nap.mod
Gfluct.o       INa_traub_shifted.o    hocload.tmp     nap.o
Gin.mod        V_m.ses                lva.mod         spike.mod
Gin.o          capump.mod             lva.o           spike.o
IKd_traub.mod  capump.o               mod_func.c      test.ses
IKd_traub.o    current.hoc            mod_func.o

[ted]

when I run the mosintsimple

How are you "running" mosinitsimple.hoc? Double click on mosinitsimple.hoc?

What happens if you double click on mosinit.hoc?

If this is from ModelDB, what is the accession number?

[firejohnx]

I have to right click and open them with neuron.exe
They both give the cant find the file response
and what is the accession number?

[ted]

what is the accession number?

Unimportant. There are more serious problems to deal with.

I have to right click and open them with neuron.exe

The big question right now is whether any aspect of NEURON works properly on your PC.

What happens if you go to the NEURON program group (under the MSWin Start menu) and select the item called
neurondemo
?

[firejohnx]

It opens up several panels
which include:
- NEURON main menu
- NEURON demonstration
- Temperature
- RunControl
- Variable Time Step

[ted]

In the
NEURON Demonstrations
panel, click on the "Release" button.
A bunch of new windows should pop up.

After these new windows have appeared, in the RunControl panel click on the "Init & Run" button. This should make a bunch of colored traces appear in the graph windows (to the right of the RunControl panel).

Did all of this happen as described?

[firejohnx]

There is no graph shown
so pushing the init & run did nothing
does that mean there are some problems?

[ted]

Exit NEURON, then start neurondemo again. What happens when you click on the Release button in the NEURON Demonstrations panel?