Search found 65 matches

by mattions
Tue Feb 23, 2010 6:58 am
Forum: UNIX/Linux
Topic: Troubles in building the nrnpython for Neuron 7.1
Replies: 2
Views: 2365

Re: Troubles in building the nrnpython for Neuron 7.1

Hi!

Actually I figured out that I was not giving the --with-nrnpython option.
that fix my setup and the installation work properly.

I misread somewhere that the python interpreter was built by default. Anyway happy ending. thanks.
by mattions
Mon Feb 22, 2010 12:09 pm
Forum: UNIX/Linux
Topic: Troubles in building the nrnpython for Neuron 7.1
Replies: 2
Views: 2365

Troubles in building the nrnpython for Neuron 7.1

Hello, I'm trying to upgrade to the latest version of Neuron. Compilation of Interview and Neuron works fine but I can't build the nrnpython. It seems the setup.py coming with the package is somehow broken (or it's not well formed in my systems) This is the error mattioni@pogo:nrnpython$ python setu...
by mattions
Wed Dec 16, 2009 11:30 am
Forum: NEURON + Python
Topic: Save the NEURON model and the geometry
Replies: 1
Views: 1192

Save the NEURON model and the geometry

Is it possible to save the model, the geometry and the simulation results with NEURON and load them again?

Using the python interpreter, in a programmatic way (not from the GUI)
by mattions
Tue Nov 24, 2009 12:31 pm
Forum: NEURON + Python
Topic: NeuronVisio: a GTK2-NEURON UI with 3D capabilities
Replies: 3
Views: 1664

Re: NeuronVisio: a GTK2-NEURON UI with 3D capabilities

version 0.3.5 out

A lot of bug fixes and new features.

Improved doc

http://mattions.github.com/neuronvisio/
by mattions
Wed Nov 04, 2009 10:58 am
Forum: Getting started
Topic: How to use a netstim to deliver several events
Replies: 2
Views: 2525

How to use a netstim to deliver several events

Hi all, I would like to use a netstim object to deliver two (or more) train of inputs. For example I would like to deliver a tstim at t=1 and t=5 netStim = h.NetStim() netStim.number = 10 netStim.start = 1 netStim.interval = 0.1 netStim.noise = 0 # NetCon obj netCon = h.NetCon(netStim, alphaSyn) net...
by mattions
Tue Oct 20, 2009 4:24 am
Forum: Parallel NEURON
Topic: Using paranrn as python module does not work
Replies: 2
Views: 2109

Re: Using paranrn as python module does not work

It works with this one.
Thanks.
by mattions
Fri Oct 09, 2009 10:22 am
Forum: Parallel NEURON
Topic: Using paranrn as python module does not work
Replies: 2
Views: 2109

Using paranrn as python module does not work

Hi, I'm trying to use the parallel neuron to run my simulation If I use the binary it works. : nrniv -python -mpi mpi_ex.py If I use neuron as python module it doesn't python mpi_exp.py The code I'm running is the following: from mpi4py import MPI import os # Removing display to import neuron proper...
by mattions
Wed Jul 29, 2009 10:49 am
Forum: Adding new mechanisms and functions to NEURON
Topic: hard limit on the lenght of an equation?
Replies: 3
Views: 1470

Re: hard limit on the lenght of an equation?

That's a good idea.
I'll try and then report back.

I'm testing an automatic translator for sbml model into NMOL with massive model. It's still a proof of concept though.
That's why there are this massive long lines with zero readibility.
by mattions
Mon Jul 27, 2009 9:43 am
Forum: Adding new mechanisms and functions to NEURON
Topic: hard limit on the lenght of an equation?
Replies: 3
Views: 1470

hard limit on the lenght of an equation?

Is there any hard limit on the lenght of an equation in a MOD file? I hit this error: Line too long: ca' = - (Spine * kon * camR * ca) - (Spine * kon * camR * ca) - (Spine * kon * camR * ca) - (Spine * kon * camR * ca) + (Spine * koffRA * camR_ca1_A) + (Spine * koffRB * camR_ca1_B) + (Spine * koffRC...
by mattions
Tue Jul 14, 2009 8:29 am
Forum: NEURON + Python
Topic: NeuronVisio: a GTK2-NEURON UI with 3D capabilities
Replies: 3
Views: 1664

Re: NeuronVisio: a GTK2-NEURON UI with 3D capabilities

version 0.3.0 out

Some BUGs fixed, better (and more responsive) handling of the animation.

http://mattions.github.com/neuronvisio/news.html
http://github.com/mattions/neuronvisio/tarball/0.3.0
by mattions
Tue Jul 14, 2009 6:53 am
Forum: NEURON + Python
Topic: Hoc Object not pickable
Replies: 1
Views: 1270

Hoc Object not pickable

Hi Forum, I would like to know if there is any plan (or if it is possible) to make the hoc Object pickable, using cPickle . This would give the possibilities to save a very complex model (vectors, sections and so on) and to reuse the model to reinvestigate the results or even continue the simulation...
by mattions
Mon Jul 06, 2009 8:25 am
Forum: NEURON + Python
Topic: NeuronVisio: a GTK2-NEURON UI with 3D capabilities
Replies: 3
Views: 1664

Re: NeuronVisio: a GTK2-NEURON UI with 3D capabilities

Version 0.2.0 out

you can select colors and an initial info tab has been added.
http://mattions.github.com/neuronvisio/news.html

Enjoy :D
by mattions
Wed Jul 01, 2009 8:40 am
Forum: NEURON + Python
Topic: NeuronVisio: a GTK2-NEURON UI with 3D capabilities
Replies: 3
Views: 1664

NeuronVisio: a GTK2-NEURON UI with 3D capabilities

Dear community, I have released the 0.1.0 http://github.com/mattions/neuronvisio/tarball/0.1.0 version of NeuronVisio http://mattions.github.com/neuronvisio/ a GTK2 User Interface with 3D capabilities for Neuron. Features * 3D visualization of the model with the possibility to change it runtime * Cr...
by mattions
Tue May 19, 2009 11:34 am
Forum: NEURON + Python
Topic: MPI4py and Neuron
Replies: 2
Views: 2572

Re: MPI4py and Neuron

we compiled with this options: ./configure --with-nrnpython --with-mpi --with-paranrn --with-x and if I run the ./configure --help this is the result mattions@triton:nrn-7.0$ ./configure --help `configure' configures nrn 7.0 to adapt to many kinds of systems. Usage: ./configure [OPTION]... [VAR=VALU...
by mattions
Mon May 18, 2009 11:45 am
Forum: NEURON + Python
Topic: MPI4py and Neuron
Replies: 2
Views: 2572

MPI4py and Neuron

I'm trying to use neuron with MPI but it seems the initialization of NEURON is not correct: mpi4py thinks I am 1 of 4, NEURON thinks I am 0 of 1 mpi4py thinks I am 2 of 4, NEURON thinks I am 0 of 1 mpi4py thinks I am 0 of 4, NEURON thinks I am 0 of 1 mpi4py thinks I am 3 of 4, NEURON thinks I am 0 o...