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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

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(...

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...

If I run `nrnpython` in python-debugger, I get the expected response. I'll try to cook up a minimal example and report it.

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 #...

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

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...

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...

Importing `gui` along with `h` seems to fix the problem.

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 else...

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...

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...

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...