Search found 13 matches

by catharina
Thu Aug 31, 2017 5:45 am
Forum: NEURON + Python
Topic: Simultaneous equations in python
Replies: 4
Views: 10802

Re: Simultaneous equations in python

Yes, that's what I tried first, see the second block of code I posted. However this doesn't give the same results as the hoc functions. So in this case the stability functions in hoc do ensure that the resting potential stays constant, but the python function doesn't.
by catharina
Wed Aug 30, 2017 11:31 am
Forum: NEURON + Python
Topic: Simultaneous equations in python
Replies: 4
Views: 10802

Re: Simultaneous equations in python

It took me a while but I finally found a way to work around it. That's the code I add in python: h('objref celllist,N') h.celllist=h.List() for elem in celllist: h.celllist.append(elem) h('proc hstab() {\n\ for nn=0,1 {\n\ rm=5e3\n\ vrest = -70\n\ //print nn\n\ dr_na = vrest-celllist.object(nn).soma...
by catharina
Wed Aug 30, 2017 5:53 am
Forum: NEURON + Python
Topic: Simultaneous equations in python
Replies: 4
Views: 10802

Simultaneous equations in python

Hi, I want to construct a network of pyramdial cells and interneuron. Therefore I have chosen to use a cell template similar to this one https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=222321. Right now I am trying to construct cell templates in python that are similar to the original o...
by catharina
Mon Aug 07, 2017 9:24 am
Forum: UNIX/Linux
Topic: Another problem using Modelview
Replies: 7
Views: 9913

Re: Another problem using Modelview

Thank you very much for your help! I have renamed the is.mod file and now the ModelView works fine! I am very pleased. The quit() issue is still there but it doesn't bother me as much. I just have to remember not to use it because sometimes its not only the gui that gets stuck but also my computer. ...
by catharina
Wed Aug 02, 2017 8:30 am
Forum: UNIX/Linux
Topic: Another problem using Modelview
Replies: 7
Views: 9913

Re: Another problem using Modelview

So for example when I download this model: https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=222321&file=/GentilettiEtAl2016/readme.html#tabs-1 I get the first error message I have posted when running it using 'nrngui mosinit.hoc' and trying to open the ModelView. And when loading it manu...
by catharina
Wed Aug 02, 2017 8:10 am
Forum: UNIX/Linux
Topic: Another problem using Modelview
Replies: 7
Views: 9913

Re: Another problem using Modelview

I think I was too fast to conclude that the Modelview problem is resolved. It still occurs! But kind of unregularly, so I cannot always reproduce it after closing all windows and starting fresh. It occurs using Spyder 3.2, IPython 5.4, Python 2.7.13 (All installed via Anaconda). It does occur when r...
by catharina
Wed Aug 02, 2017 6:10 am
Forum: UNIX/Linux
Topic: Another problem using Modelview
Replies: 7
Views: 9913

Re: Another problem using Modelview

I have now installed NEURON 7.5. It did go almost smoothly and the Modelview error does resolve!

However the error when using the quit button of the gui still occurs whenever the gui is opened with Ipython but not when opened with python.
by catharina
Tue Aug 01, 2017 6:37 am
Forum: UNIX/Linux
Topic: Another problem using Modelview
Replies: 7
Views: 9913

Another problem using Modelview

Hello, since updating spyder to the newest version using 'conda update spyder', the NEURON Gui crashes and gets stuck whenever I try to open the ModelView. This happens using the nrngui -python from the command line and also when I use spyder to run python files with neuron using spyder. This also h...
by catharina
Tue Jul 11, 2017 6:23 am
Forum: NEURON + Python
Topic: Section of source for h. NetCon() in Python
Replies: 2
Views: 9576

Re: Section of source for h. NetCon() in Python

Hi, Thank you very much for you fast reply and also the comments on my code! I wasn't aware of this bracket convention but that obviously makes things way easier. Indeed I am using a IPython (in spyder) to run my python scripts together with NEURON 7.4 incorporated as a python package. Is there a si...
by catharina
Mon Jul 10, 2017 11:52 am
Forum: NEURON + Python
Topic: Section of source for h. NetCon() in Python
Replies: 2
Views: 9576

Section of source for h. NetCon() in Python

Hello, I am trying to connect instances of a very simple cell class SimpCell() with NetCons. I am working in python but the cell class SimpCell() is defined in a hoc file and I would like to keep the cell template in hoc. I am able to create NetCon with a NONE source using "netcon = h.NetCon(None, c...
by catharina
Fri Jun 23, 2017 10:58 am
Forum: Modeling networks
Topic: Combining NEURON with a mesoscale equation
Replies: 4
Views: 6298

Re: Combining NEURON with a mesoscale equation

Dear Ted,

Thank you very much for your tips so far!

I am going to go ahead and Implement the model in the following weeks. Now I am more optimistic that I can succeed and cython will definitely make it easier for me!

Best regards, Catharina
by catharina
Mon Jun 19, 2017 11:05 am
Forum: Modeling networks
Topic: Combining NEURON with a mesoscale equation
Replies: 4
Views: 6298

Re: Combining NEURON with a mesoscale equation

Hi Ted, thank you for replying and your opinion! The mesoscopic equation that I want to integrate with NEURON is the kuramoto equation. To start with I have decided to implement a very simplified version of it, whereby the voltage change over time dV/dt of each cell i is described by dV_i/dt = w_i +...
by catharina
Fri Jun 16, 2017 10:44 am
Forum: Modeling networks
Topic: Combining NEURON with a mesoscale equation
Replies: 4
Views: 6298

Combining NEURON with a mesoscale equation

Hello, I need advise on how to combine NEURON with a mesoscopic equation (ODE). I have built a network of simple cells (soma + dendrite with synapses) in NEURON using mainly python. The cells are connected with excitatory synapses (ExpSyn). I have chosen the cell properties in such a way that each c...