Search found 16 matches

by sohaib786
Tue Oct 06, 2020 1:20 pm
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 379

Re: Installing on Ubuntu 20.04 (GUI not working)

The error which I posted is from 7.6.7.

Code: Select all

from neuron import h
is working. But the GUI doesn't pop up, but it gives the output which I shared in the first post.
by sohaib786
Sun Oct 04, 2020 1:55 pm
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 379

Re: Installing on Ubuntu 20.04 (GUI not working)

After using sudo pip3 install neuron, it did the installation(successfully) but didn't work. This is its location. It is still present. neuron in /usr/local/lib/python3.8/dist-packages (7.8.1.1) I then installed using tar.gz file of 7.6.7 version of nrn and iv, which I had downloaded some days back ...
by sohaib786
Sun Oct 04, 2020 8:22 am
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 379

Installing on Ubuntu 20.04 (GUI not working)

Hi, After installing the package I wanted to run the gui for which I wrote in the terminal- nrngui -python This gave the following error- Duke, Yale, and the BlueBrain Project -- Copyright 1984-2018 See http://neuron.yale.edu/neuron/credits /home/sohaib/neuron/nrn/x86_64/bin/nrniv: Couldn't find: st...
by sohaib786
Thu Mar 28, 2019 4:30 pm
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 11455

Re: Morphology and AP generation

Do you see a problem with iteration over segments when you just use Python from NEURON, without Jupyter? Had not tried before. However, upon checking, it works fine with just python. In both cases, i.e Loading with or without GUI doesn't affect it and works fine. Jupyter seems to create some troubl...
by sohaib786
Tue Mar 26, 2019 1:49 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 11455

Re: Morphology and AP generation

email that zip file
Thanks. Sure.
what version of
NEURON is being used by the notebook
Neuron Version : NEURON -- VERSION 7.5 master (6b4c19f) 2017-09-25
Anaconda: Version 5.2.0 , Build Channel- py36_3
by sohaib786
Mon Mar 25, 2019 4:53 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 11455

Re: Morphology and AP generation

You should get something like this I do get like this. But intriguingly, sometimes it doesn't print all of them. Also sometimes, when i load a file such as this. from neuron import h h.load_file('/home/sohaib/neuron/ASC Files/fmc3_1') h.load_file('/home/sohaib/neuron/ASC Files/fmc3_1') (fmc3_1 is a...
by sohaib786
Sun Mar 24, 2019 12:55 pm
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 11455

Re: Morphology and AP generation

Two things happen when this command is run. for sec in h.allsec(): for seg in sec: print(seg) It prints soma(0.5) dend[0](0.5) dend[1](0.5) dend[2](0.5) dend[3](0.5) so on and so forth But sometime it prints soma(0.5) dend[0](0.1) dend[0](0.3) dend[0](0.5) dend[0](0.9) dend[1](0.1) dend[1](0.3) dend...
by sohaib786
Sat Mar 23, 2019 1:30 pm
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 11455

Re: Morphology and AP generation

I tried doing a weighted compartment analysis. However, I checked some of the parameters of all the dendrites to get an idea and found this problem. I took a dendrite randomly and enquired into its segments and their morphological parameters. x = h.dend[2] for i in x.allseg(): print(i, i.area(), i.d...
by sohaib786
Fri Mar 22, 2019 6:19 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 11455

Re: Morphology and AP generation

That was really insightful. By Excitability, I meant that the cell may report a higher number of AP's by a reduction in the threshold, reduced spike interval, or increased amplitude of Vsoma. The reason for this view is because REM sleep deprivation has been hypothesized to increase cell excitabilit...
by sohaib786
Tue Mar 19, 2019 9:14 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 11455

Re: Morphology and AP generation

I am trying to study the effect of the altered structure on cell function caused due to REM sleep deprivation. I have morphology for both control and treatment group, and I am using biophysical properties of the control group. I am exciting a single dendrite at its midpoint and checking voltage at t...
by sohaib786
Tue Mar 12, 2019 2:29 am
Forum: NEURON + Python
Topic: BioPhysical properties of imported morphology in Python
Replies: 9
Views: 2590

Re: BioPhysical properties of imported morphology in Python

No it doesn't. It does seem to load the hoc file. I accessed details like h.soma.Ra which it reported the value I had put in earlier. I also ran a simulation placing an I clamp at a different dendritic positions and it generated spike perfectly. Read the Programmer's Reference documentation of load...
by sohaib786
Mon Mar 11, 2019 3:40 pm
Forum: NEURON + Python
Topic: BioPhysical properties of imported morphology in Python
Replies: 9
Views: 2590

Re: BioPhysical properties of imported morphology in Python

This particular command generates the following error. from neuron import h h.load_file("/home/sohaib/neuron/mycell.hoc") Couldn't find: /home/sohaib/neuron/mycell.hoc near line 0 objref hoc_obj_[2] However, running this command twice does it. from neuron import h h.load_file('/home/sohaib/neuron/my...
by sohaib786
Mon Mar 11, 2019 3:49 am
Forum: NEURON + Python
Topic: BioPhysical properties of imported morphology in Python
Replies: 9
Views: 2590

Re: BioPhysical properties of imported morphology in Python

I wasn't telling you to literally try to load mycell.hoc. I was just providing an example of how to use load_file to read a hoc file, so I needed a name for a hoc file and I just made one up
I understood that, so I renamed my file as mycell just to maintain coherency.

Thanks anyways.
by sohaib786
Sun Mar 10, 2019 6:16 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 11455

Morphology and AP generation

Greetings all, I am interested in finding out the difference, morphology could have on the generation of AP. In its perusal, I wrote a code using neuron GUI + python for exciting at distal synapses and generating AP. ( Action Potential) The problem is that if we provide stimulus at different positio...
by sohaib786
Fri Mar 08, 2019 2:15 am
Forum: NEURON + Python
Topic: BioPhysical properties of imported morphology in Python
Replies: 9
Views: 2590

Re: BioPhysical properties of imported morphology in Python

Apologies for not specifying properly. ca3fin was the hoc file created after importing morphology & adding biophysical properties. Also, using this it imported successfully (without .hoc extension) h.load_file('/home/sohaib/neuron/mycell') . The unusual part is that on the first attempt of running t...