Calcium diffusion and shells

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ziemek
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Calcium diffusion and shells

Post by ziemek » Thu Nov 14, 2019 7:41 am

Hi there,

Is there any easy way to implement in NEURON a Calcium diffusion with shells similar in concept to the figure 6.8 from the Principles of Computational Modelling in Neuroscience, Sterrat et al. :
https://drive.google.com/file/d/13YeDmG ... PVVdB/view (image)

I would be very glad for your help :)

ted
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Re: Calcium diffusion and shells

Post by ted » Thu Nov 14, 2019 8:20 am

See chapter 9 of the NEURON Book. If you don't have the book, get this preprint
https://www.neuron.yale.edu/ftp/ted/boo ... xedref.pdf
If you installed NEURON from source code, see
nrn/share/examples/nrniv/nmodl/cadif.mod
which may be slightly different from the example in the book. If you didn't install from source code, suggest you get the source code files anyway and check out the examples in that directory.

ziemek
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Location: Warsaw, Poland
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Re: Calcium diffusion and shells

Post by ziemek » Tue Nov 19, 2019 7:27 am

Thanks for help. Unfortunatelly there is an error while I make

Code: Select all

nrnivmodl

Code: Select all

"/usr/local/nrn/share/nrn/libtool" --tag=CC --mode=link gcc -module  -g -O2    -o libnrnmech.la -rpath "/usr/local/nrn/x86_64/lib"  cadif.lo mod_func.lo  -L"/usr/local/nrn/x86_64/lib" -lnrnoc -loc -lmemacs  -lscopmath -lsparse13 -lreadline -lncurses -ltinfo -L"/usr/local/nrn/x86_64/lib" -lnrniv -livoc -lneuron_gnu -lmeschach -lsundials       -lm -ldl
libtool: link: gcc -shared  -fPIC -DPIC  .libs/cadif.o .libs/mod_func.o   -Wl,-rpath -Wl,/usr/local/nrn/x86_64/lib -Wl,-rpath -Wl,/usr/local/nrn/x86_64/lib -L/usr/local/nrn/x86_64/lib /usr/local/nrn/x86_64/lib/libnrnoc.so /usr/local/nrn/x86_64/lib/liboc.so -lX11 /usr/local/nrn/x86_64/lib/libmemacs.so /usr/local/nrn/x86_64/lib/libscopmath.so /usr/local/nrn/x86_64/lib/libsparse13.so -lreadline -lncurses -ltinfo /usr/local/nrn/x86_64/lib/libnrniv.so /usr/local/nrn/x86_64/lib/libivoc.so /usr/local/nrn/x86_64/lib/libneuron_gnu.so /usr/local/nrn/x86_64/lib/libmeschach.so /usr/local/nrn/x86_64/lib/libsundials.so -lm -ldl  -g -O2   -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0
/usr/bin/ld: cannot find -lreadline
collect2: error: ld returned 1 exit status
I have NEURON ver. 7.7.2 and the cadif.mod file come from today's master branch of NEURON from GitHub.

But it does work well with ver 7.5 and older (7.6 though still doesn't work).

Do you have any clue how to fix it?

ted
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Re: Calcium diffusion and shells

Post by ted » Tue Nov 19, 2019 9:43 am

Check to see if the readline library exists on your computer. If it doesn't, download and install it, then uninstall and reinstall NEURON.

How? Depends on your Linux distribution. For distributions that use rpm for package management,
rpm -q readline
and
rpm -ivh readline
are your friends.
Debian-related distributions use dpkg and apt--read the relevant documentation.

ziemek
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Location: Warsaw, Poland
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Re: Calcium diffusion and shells

Post by ziemek » Wed Nov 20, 2019 9:51 am

Thanks, indeed readline did the trick.

If anyone has the same problem in the future - this answer may help: https://askubuntu.com/questions/194523/ ... u-readline

ted
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Re: Calcium diffusion and shells

Post by ted » Wed Nov 20, 2019 10:36 am

Thanks, that will be a useful tip for others who may read this thread.

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