reuse modelDB:84589

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Sun Xiaoqing
Posts: 32
Joined: Wed Aug 28, 2019 1:18 am

reuse modelDB:84589

Post by Sun Xiaoqing » Sun Sep 22, 2019 1:00 am

Hi,

I'm trying to reuse the Extracellular Action Potential Simulation from:
https://senselab.med.yale.edu/ModelDB/S ... 589#tabs-1
It was implemented in 2006, and some code didn't work right now. I also have tried to create my own model by combining different parts from the other models which I found it very difficult to achieve.

I'm using Win10 and by typing cmd:

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c:\eaps>c:\nrn\bin\neuron.exe -dll mod\nrnmech.dll hoc/src/refs.hoc cells/d151.hoc hoc/src/main.hoc
These messages showed:

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c:\eaps>NEURON -- VERSION 7.7.2 7.7 (2b7985ba) 2019-06-20
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2018
See http://neuron.yale.edu/neuron/credits

loading membrane mechanisms from mod/nrnmech.dll
Additional mechanisms from files
 cadif.mod cal.mod can.mod car.mod cat.mod hdend.mod hsoma.mod kadist.mod kahp.mod kaprox.mod kc.mod kd.mod kk.mod km.mod naf.mod nax.mod
LOADING GEOMETRY FOR d151

-> Setting file roots...
C:\nrn\bin\nrniv.exe: set_file_roots undefined function
 in hoc/src/main.hoc near line 121
 set_file_roots()
I was able to compile the mod file and it seemed like the Geometry of the cell was also successfully loaded. I tried to revise it but didn't work out.
Can anyone give me some advice? Thanks.

Kind regard,
SUN XIAOQING

Sun Xiaoqing
Posts: 32
Joined: Wed Aug 28, 2019 1:18 am

Re: reuse modelDB:84589

Post by Sun Xiaoqing » Sun Sep 22, 2019 9:42 am

I also got another confusion that when I double click on eaps\cell\d151.hoc, I got these error messages:

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NEURON -- VERSION 7.7.2 7.7 (2b7985ba) 2019-06-20
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2018
See http://neuron.yale.edu/neuron/credits

Could not open C:/Users/sunxi/AppData/Roaming/Microsoft/Windows/Start Menu/Programs/Anaconda3 (64-bit)/Anaconda Prompt.lnk
Could not open C:/Users/sunxi/AppData/Roaming/Microsoft/Windows/Start Menu/Programs/Anaconda3 (64-bit)/Anaconda Prompt.lnk
Cannot find executable python3 or python
C:\nrn\bin\nrniv.exe: syntax error
 in C:/eaps/cells/d151.hoc near line 8
 neuron_name = "d151"
After deleting the statements from the start:

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neuron_name = "d151"
cell_type = "ca1pyr"
Error messages also showed up like this:

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NEURON -- VERSION 7.7.2 7.7 (2b7985ba) 2019-06-20
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2018
See http://neuron.yale.edu/neuron/credits

Could not open C:/Users/sunxi/AppData/Roaming/Microsoft/Windows/Start Menu/Programs/Anaconda3 (64-bit)/Anaconda Prompt.lnk
Could not open C:/Users/sunxi/AppData/Roaming/Microsoft/Windows/Start Menu/Programs/Anaconda3 (64-bit)/Anaconda Prompt.lnk
Cannot find executable python3 or python
LOADING GEOMETRY FOR d151
oc>     -65
However, I was able to choose from Tools\Shape Plot, The d151 cell was the correct shape.

When I double clicked on nrniv_python, no error messages showed up, then why I still got :

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Could not open C:/Users/sunxi/AppData/Roaming/Microsoft/Windows/Start Menu/Programs/Anaconda3 (64-bit)/Anaconda Prompt.lnk
Could not open C:/Users/sunxi/AppData/Roaming/Microsoft/Windows/Start Menu/Programs/Anaconda3 (64-bit)/Anaconda Prompt.lnk
Cannot find executable python3 or python
Sorry for my relative basic questions, I'd appreciate it if you can give me some advice or suggesting some reference book or posts which I can solve this problem. Thank you.

ted
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Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Re: reuse modelDB:84589

Post by ted » Thu Sep 26, 2019 6:38 pm

Tom Morse, curator of ModelDB, has revised this model entry so that it works under MSWin and is easier to launch (including enabling "auto-launch" to work). He has also revised the README.html file accordingly. Many thanks, Tom!

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