Search found 13 matches

by dilawar
Mon Jul 06, 2015 4:52 am
Forum: Anatomically detailed models
Topic: Inserting channels (some distribution) after loading SWC fil
Replies: 3
Views: 6437

Re: Inserting channels (some distribution) after loading SWC

Thanks,

I managed to load the SWC file using python interface. Then I inserted few ion-channels into the model. To be sure, I want to count the number of channels to check my mechanism is getting inserted or not. How to get the number of compartment and channels using nrnpython?

best,
Dilawar
by dilawar
Thu May 07, 2015 2:30 am
Forum: NEURON + Python
Topic: Monitoring injected current in a segment
Replies: 6
Views: 2417

Re: Monitoring injected current in a segment

Dear Ted, I'll create a toy example. Meanwhile, replacing following lines, stim = h.IClamp(0.5, sec=section) stim.amp = 0.1 stim.dur = float(1e3*_args.sim_time) with following lines did the trick. h('access %s' % section.hname()) h('objectvar stim') h('stim = new IClamp(0.5)') h('stim.amp = 0.1') h(...
by dilawar
Wed May 06, 2015 3:16 am
Forum: NEURON + Python
Topic: Monitoring injected current in a segment
Replies: 6
Views: 2417

Re: Monitoring injected current in a segment

Unfortunately the script I have do things which are bit involved: 1. It reads a given SWC file and loads it into NEURON. 2. It builds the topology of network (using python-networkx). 3. It inserts the channels into cell according to a given distribution. 4. It stimulate the cell for a second and plo...
by dilawar
Wed May 06, 2015 2:58 am
Forum: NEURON + Python
Topic: Monitoring injected current in a segment
Replies: 6
Views: 2417

Re: Monitoring injected current in a segment

If I run `nrnpython` in python-debugger, I get the expected response. I'll try to cook up a minimal example and report it.
by dilawar
Tue May 05, 2015 8:05 am
Forum: NEURON + Python
Topic: Monitoring injected current in a segment
Replies: 6
Views: 2417

Monitoring injected current in a segment

In my nrnpython model, I am dealing with an issue. Response of my cell is independent of current I inject into `soma`. To check what is really going on, I want to monitor injected current into soma. def addStim(section): """Setup the stimulus""" global _args, _records # _records is a dictionary. pri...
by dilawar
Fri May 01, 2015 1:34 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Import or conversion of ChannelML(NeuronML-1.8) for NEURON
Replies: 5
Views: 7367

Re: Import or conversion of ChannelML(NeuronML-1.8) for NEUR

Yes. It loads them without loading the .so file. I was using a snippet from some thread on the forum without reading the context carefully.

Thanks for all your help. I really appreciate quick response I get on this forum.

- D
by dilawar
Thu Apr 30, 2015 2:51 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Import or conversion of ChannelML(NeuronML-1.8) for NEURON
Replies: 5
Views: 7367

Re: Import or conversion of ChannelML(NeuronML-1.8) for NEUR

Thank you ramcdougal and ted. After compiling mechanism and loading them into nrnpython using `nrn_load_dll``, I managed to insert these mechanisms. Unfortunately I have to code platform specific path e.g. `nrn_load_dll('./i686/.lib/xxx')` or `nrn_load_dll('x86_64/.lib/xxx'). Is there a more portabl...
by dilawar
Tue Apr 28, 2015 9:02 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Import or conversion of ChannelML(NeuronML-1.8) for NEURON
Replies: 5
Views: 7367

Import or conversion of ChannelML(NeuronML-1.8) for NEURON

A few channel-mechanism I have are in channelML format. Is there a way to directly import them into NEURON (version 7.4)? Or any program which can convert these XML file to NEURON format? PS: There is one here: http://www.neuroml.org/neuron_tools , but it doesn't seem to work. Header generated by th...
by dilawar
Sun Apr 26, 2015 2:00 am
Forum: NEURON + Python
Topic: Error on loading the SWC file using neuron
Replies: 2
Views: 1939

Re: Error on loading the SWC file using neuron

Importing `gui` along with `h` seems to fix the problem.
by dilawar
Sat Apr 25, 2015 2:14 pm
Forum: NEURON + Python
Topic: Error on loading the SWC file using neuron
Replies: 2
Views: 1939

Error on loading the SWC file using neuron

I am using the following script to load a SWC file. I am using Neuron-7.4 build from source code. from neuron import h import sys def instantiate_swc(filename): """load an swc file and instantiate it""" # load the NEURON library (just in case h is defined otherwise elsewhere) # a helper library, inc...
by dilawar
Fri Apr 10, 2015 9:13 am
Forum: Anatomically detailed models
Topic: Inserting channels (some distribution) after loading SWC fil
Replies: 3
Views: 6437

Inserting channels (some distribution) after loading SWC fil

I was searching if one can specify channel distribution once a cell is created by loading SWC file into NEURON. I am thinking of specifying a region of cell and distribution of channel by an expression valid in that region. I am using Neuron-7.4 with python support enabled. Is there a snippet/exampl...
by dilawar
Wed May 28, 2014 12:37 am
Forum: Modeling networks
Topic: Rallpack3 is producing slightly different results
Replies: 3
Views: 5812

Re: Rallpack3 is producing slightly different results

The benchmarks are available here http://genesis-sim.org/node/127. After extraction, go to 'reports/rallpack3/neuron' folder. I am also not sure which NEURON was used in these benchmarks. However, changing gl to gl_hh fixed the issue. Also I added finitialize() before run(). I would be cool if NEURO...
by dilawar
Tue May 27, 2014 1:15 am
Forum: Modeling networks
Topic: Rallpack3 is producing slightly different results
Replies: 3
Views: 5812

Rallpack3 is producing slightly different results

Hi, I am running Rallpacks benchmark (http://www.ncbi.nlm.nih.gov/pubmed/1281353) with Neuron. The reference benchmark came with NEURON and GENSIS scripts. I modified the NEURON script for NEURON7.x. The reference contains a cable with 1000 compartments. Each compartment having HH-type Na and K chan...