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New reaction-diffusion model on ModelDB
Posted: Thu Dec 18, 2014 1:23 pm
by samnemo
A new paper,
Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model, was recently accepted to
Neural Computation.
The paper describes an electrochemical model that uses NEURON's new reaction-diffusion features, and may therefore serve as a template for other projects.
The model is avaiable here:
http://senselab.med.yale.edu/modeldb/Sh ... del=168874
The manuscript is available here:
http://neurosimlab.org/publications.html
Questions or comments are welcome.
Re: New reaction-diffusion model on ModelDB
Posted: Thu Jan 08, 2015 12:34 am
by tardebut
Thanks.
Omar
Re: New reaction-diffusion model on ModelDB
Posted: Fri Apr 03, 2015 2:54 am
by Darshan
Hi,
Thanks for making the model available on ModelDb. I tried using the code by following the instructions in readme file. The mod files get compiled correctly. But when I run this
I get the following error:
Code: Select all
File "cawave.py", line 183, in <module>
cyt_er_membrane = rxd.Region(h.allsec(), geometry=rxd.ScalableBorder(1))
AttributeError: 'module' object has no attribute 'ScalableBorder'
I checked the library 'rxd' and I couldn't locate the function ScalableBorder(). Where can I get this function? If I keep the parameter 'geometry = None' or 'geometry = rxd.FractionalVolume(fe)', then another error comes saying that
Code: Select all
must specify a membrane not a volume for the boundary.
The NEURON version I am using is 7.3 ansi (1078:2b0c984183df).
Thanks,
Darshan
Re: New reaction-diffusion model on ModelDB
Posted: Fri Apr 03, 2015 11:20 am
by ted
Darshan wrote:The NEURON version I am using is 7.3 ansi (1078:2b0c984183df).
That may be the cause of the problem. There have been many bug fixes and updates since then. If you are compiling NEURON from source code, suggest you get the latest development code from its mercurial repository. If instead you are using a precompiled installer, get one of the most recent alpha versions from
http://www.neuron.yale.edu/ftp/neuron/versions/alpha/
If you use MSWin and want to use your own Python, get the mingw-based installer. Otherwise get the cygwin-based installer.
Re: New reaction-diffusion model on ModelDB
Posted: Sat Apr 04, 2015 6:14 am
by Darshan
Hi Ted,
Thanks for the quick reply. I compiled using the latest source code from the repository. Now, the first line on starting NEURON reads: NEURON -- VERSION 7.4 (1315:a35e721080fb) 2015-04-02.
I compiled the code with nrnivmodl and it was successful with a few warnings. A seperate folder called 'x86_64' is created with the .mod, .c and .o files. Then, I tried running the code as mentioned in my previous post. But, I still get the exact same error. On checking the rxd library, 'rxd.ScalableBorder' was not found (see below for the available funtions):
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In [3]: rxd.
rxd.FixedCrossSection rxd.morphology
rxd.FixedPerimeter rxd.multiCompartmentReaction
rxd.FractionalVolume rxd.node
rxd.MultiCompartmentReaction rxd.nodelist
rxd.Parameter rxd.options
rxd.Rate rxd.rate
rxd.Reaction rxd.re_init
rxd.Region rxd.reaction
rxd.Shell rxd.region
rxd.Species rxd.rxd
rxd.State rxd.rxdmath
rxd.generalizedReaction rxd.rxdsection
rxd.geometry rxd.scipy
rxd.inside rxd.section1d
rxd.membrane rxd.species
Another question, related to compiling source files: Is it possible to update the existing compiled code on a system with the latest source code available in mercurial repository without having to uninstall and then compile the source code again?
Re: New reaction-diffusion model on ModelDB
Posted: Mon Apr 06, 2015 12:52 pm
by ramcdougal
Your system is somehow finding the old Python library. When you compile, after the "sudo make install" try: "cd src/nrnpython" and "sudo python setup.py install".
As far as compiling goes: if you're replacing a version built from the repository, then yes, you can safely do a "hg pull -u", "make", "sudo make install", "cd src/nrnpython", "sudo python setup.py install".
Re: New reaction-diffusion model on ModelDB
Posted: Tue Apr 07, 2015 3:55 pm
by Darshan
Thanks Robert. It was actually taking the old python library. The reason for that was incorrect PYTHONPATH.
Another error came up after this, which was because of unavailability of cython(pointed out by Robert. Thanks!). It was corrected by installing it using
and then compiling the code again using:
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./configure --with-nrnpython
make
sudo make install
cd src/nrnpython
sudo python setup.py install
After doing this, the model was working correctly.