Search found 48 matches

by roybens
Tue Jul 21, 2020 12:40 pm
Forum: NEURON + Python
Topic: color or color_list procedures in PlotShape
Replies: 5
Views: 434

Re: color or color_list procedures in PlotShape

Thanks so much!
This is very helpful.
by roybens
Thu Jul 16, 2020 11:42 pm
Forum: NEURON + Python
Topic: color or color_list procedures in PlotShape
Replies: 5
Views: 434

Re: color or color_list procedures in PlotShape

Hi ramcdougal, I am probably doing something wrong or there is a problem in my environment (though for any other purpose except this it is working totally fine) So i tried the code you sent on both my local machine (running windows NEURON 7.7) and i get the following error: runfile('E:/GitHub/MoreGi...
by roybens
Tue Jul 07, 2020 5:59 pm
Forum: NEURON + Python
Topic: color or color_list procedures in PlotShape
Replies: 5
Views: 434

Re: color or color_list procedures in PlotShape

This is very helpful,
I will try both methods, and report back if I get into any problems.
Thanks ramcdougal!
by roybens
Mon Jul 06, 2020 4:58 pm
Forum: NEURON + Python
Topic: color or color_list procedures in PlotShape
Replies: 5
Views: 434

color or color_list procedures in PlotShape

Hi, I am trying to plot the morphology of a neuron with a different color for each section. I am trying to use the PlotShape (really nice it is working with matplotlib now). The code i am running is: from neuron import h from matplotlib import pyplot mosinit_hoc = '/global/homes/r/roybens/Cori/Neuro...
by roybens
Fri Feb 01, 2019 12:41 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 2503

Re: eca calculation

Thanks Micheal,
Now the results i got from ion_style does make sense.
Best
Roy
by roybens
Thu Jan 31, 2019 5:54 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 2503

Re: eca calculation

:-) thanks Ted, ill continue investigating!
by roybens
Thu Jan 31, 2019 2:40 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 2503

Re: eca calculation

I am a bit confused trying to figure this out. From the program reference i get this: The oldstyle value is previous internal setting of c_style + 4*cinit + 8*e_style + 32*einit + 64*eadvance. c_style: 0, 1, 2, 3. Concentrations respectively treated as UNUSED, PARAMETER, ASSIGNED, or STATE variables...
by roybens
Thu Jan 31, 2019 1:54 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 2503

Re: eca calculation

Thank, Ted!
This is very helpful.
by roybens
Wed Jan 30, 2019 7:01 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 2503

eca calculation

Hi, I wanted to ask how does NEURON knows when to calculate eca from cai and cao or not to. For example in Mainen's model https://senselab.med.yale.edu/modeldb/showmodel.cshtml?model=2488&file=%2Fcells%2F#tabs-1 the eca is always 140. But when using one of the BBP models from their portal it is upda...
by roybens
Fri Jun 15, 2018 4:23 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 7657

Re: Getting the full topology (segments level) from hoc

Hi again, I am back in trying to apply this method on a more complicated model - one of the BBP pyramidal neurons https://bbp.epfl.ch/nmc-portal/downloads. For some reason when applying this method to Mainen's model (1996) it works well but when applying to BBP it does not work at all and it is like...
by roybens
Sat Mar 11, 2017 5:38 pm
Forum: UNIX/Linux
Topic: Running neuron with MPI using debian package
Replies: 1
Views: 8952

Running neuron with MPI using debian package

Hi, I am trying to use neuron on a cluster without shared libraries we used the debian package as shifter image and NEURON is runnig well. The problem is when i am trying to use MPI i get only one process. I am trying to use the simple example from the parallelcontext documentation i get nprocs=1 My...
by roybens
Sat Mar 11, 2017 5:33 pm
Forum: UNIX/Linux
Topic: configuring on supercomputer/cluster without shared libs
Replies: 2
Views: 9427

Re: configuring on supercomputer/cluster without shared libs

Thanks!
We eventually used a shifter image using the debian package at http://www.neuron.yale.edu/ftp/neuron/v ... x86_64.deb
by roybens
Thu Jan 05, 2017 11:57 am
Forum: UNIX/Linux
Topic: configuring on supercomputer/cluster without shared libs
Replies: 2
Views: 9427

configuring on supercomputer/cluster without shared libs

Hi, I am trying to build neuron with mpi on supercomputer where we cannot use shared libraries. So building NEURON itself goes smoothly when i use the following configure: ./configure --prefix=`pwd` --with-paranrn --without-iv --enable-shared=no CC=cc CXX=CC But then when i want to add mod file and ...
by roybens
Fri Sep 30, 2016 5:44 pm
Forum: MSWin
Topic: Trying to print _rhs using gdb
Replies: 5
Views: 10264

Re: Trying to print _rhs using gdb

Ha! it worked Thanks!!
by roybens
Fri Sep 30, 2016 3:43 pm
Forum: MSWin
Topic: Trying to print _rhs using gdb
Replies: 5
Views: 10264

Re: Trying to print _rhs using gdb

So i should have mentioned it in the first post, I am using bash on windows - which is a ubuntu linux shell on windows 10 (pretty new feature for win) And i go to '~/neuron/nrn/x86_64/bin$' and run gdb nrniv from there. When trying to set a breakpoint at nrn_rhs i cannot typing (gdb) break nrn (then...