Search found 43 matches

by ziemek
Tue Dec 03, 2019 3:06 am
Forum: NEURON + Python
Topic: Shape plot update from Python
Replies: 2
Views: 684

Re: Shape plot update from Python

It works straight forward. Thanks!
by ziemek
Mon Dec 02, 2019 1:22 pm
Forum: NEURON + Python
Topic: Shape plot update from Python
Replies: 2
Views: 684

Shape plot update from Python

I would like to monitor "cai" variable across shape plot. After I execute this code it shows correctly what I want to monitor, except that it wont update with each steps: ps = h.PlotShape(True) ps.variable('cai') ps.scale(0, 0.01) ps.show(0) ps.exec_menu('Shape Plot') When I specify the same paramet...
by ziemek
Sat Nov 30, 2019 4:31 am
Forum: Adding new mechanisms and functions to NEURON
Topic: using diam and L params inside MODL file
Replies: 5
Views: 972

Re: using diam and L params inside MODL file

Thanks for your help and comments, they are very valuable to me. I started with RxD and it works nice but I have 4 follow-up questions and one comment. Questions: if you don't specify geometry for the Region - it assumes the whole compartment's segment as a "single shell"? If I do specify geometry -...
by ziemek
Tue Nov 26, 2019 5:26 am
Forum: Adding new mechanisms and functions to NEURON
Topic: using diam and L params inside MODL file
Replies: 5
Views: 972

Re: using diam and L params inside MODL file

OK, so I would like to model Ca2+ radial diffusion from the top of the head of the dendritic spine -> through the neck -> to the dendrite (and in the dendrite radially and axially - as well, so Ca2+ may diffuse to the next spine). Basically I would like to model a whole-cell Ca2+ diffusion. EDIT: I ...
by ziemek
Mon Nov 25, 2019 11:16 am
Forum: Adding new mechanisms and functions to NEURON
Topic: using diam and L params inside MODL file
Replies: 5
Views: 972

using diam and L params inside MODL file

Hi, I want to use compartment's params (diam, L) inside my MODL mechanism "mymodl": NEURON { SUFFIX mymodl } UNITS { (um) = (micron) } ASSIGNED { diam (um) L (um) } STATE { my_diam (um) my_L (um) } BREAKPOINT { my_diam = diam my_L = L } hoc file looks like that: load_file("nrngui.hoc") create soma a...
by ziemek
Mon Nov 25, 2019 6:16 am
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL: COMPARTMENT statement in the KINETIC section
Replies: 2
Views: 528

Re: NMODL: COMPARTMENT statement in the KINETIC section

You're right. After I carefully studied chapters 3 and 9 I got it. For those who may have similar questions - please read first: Compartment size in the section on Chemical reactions in Chapter 3 and then get back to the Chapter 9 . As to answer my questions (if anyone has similar problems): 1/4. CO...
by ziemek
Thu Nov 21, 2019 7:47 am
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL: COMPARTMENT statement in the KINETIC section
Replies: 2
Views: 528

NMODL: COMPARTMENT statement in the KINETIC section

From the Neuron Book, chapter 9. Ca2+ shells diffusion is defined as follows: KINETIC state { COMPARTMENT i, diam*diam*vol[ i ] {ca CaBuffer Buffer} } How does the COMPARTMENT statement work? Why there is diam^2? What is its relation to the volume? if shell_volume=diam*diam*vol[ i ] -> does the rate...
by ziemek
Wed Nov 20, 2019 9:51 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Calcium diffusion and shells
Replies: 5
Views: 761

Re: Calcium diffusion and shells

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
by ziemek
Tue Nov 19, 2019 7:27 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Calcium diffusion and shells
Replies: 5
Views: 761

Re: Calcium diffusion and shells

Thanks for help. Unfortunatelly there is an error while I make nrnivmodl "/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 -lrea...
by ziemek
Thu Nov 14, 2019 7:41 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Calcium diffusion and shells
Replies: 5
Views: 761

Calcium diffusion and shells

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/13YeDmGO26dwu-T63HEbbae_K6BQPVVdB/view (image) I would be very ...
by ziemek
Thu Oct 31, 2019 12:21 pm
Forum: UNIX/Linux
Topic: PyNeuron + Ubuntu + Python 3.6
Replies: 5
Views: 2116

Re: PyNeuron + Ubuntu + Python 3.6

Well obviously I did it after a fresh installation of NEURON Python couldn't find the neuron library, that's the problem. I use Anaconda, but it shouldn't be an issue. After I downloaded the source code from the github, compile it and then install nrnpython by hand - it finally started to work :) Bu...
by ziemek
Thu Oct 31, 2019 10:48 am
Forum: UNIX/Linux
Topic: PyNeuron + Ubuntu + Python 3.6
Replies: 5
Views: 2116

Re: PyNeuron + Ubuntu + Python 3.6

Thank's for quick answer, but is there any supported way to use NEURON with Python? Well, at least according to this simple QuickStart: https://www.neuron.yale.edu/ftp/neuron/2019umn/neuron-quickstart.pdf after a fresh NEURON installation Python libs should just work, but not for me since I have: >>...
by ziemek
Thu Oct 31, 2019 10:05 am
Forum: UNIX/Linux
Topic: PyNeuron + Ubuntu + Python 3.6
Replies: 5
Views: 2116

PyNeuron + Ubuntu + Python 3.6

Hi there, I Try to install neuron for Python on Ubuntu 16.04 and Python 3.6 with command: pip install neuron but I received this error: Only Windows and 64-bit Linux currently supported by PyNEURON The error is strange since I have 64-bit Ubuntu. Then I tried with: pip install pyneuron and now the e...