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 plot the results in nrn.eps file.
between step 3 and step 4, I inject some current into soma (see function `addStim` in script `loader_neuron.py`, line number 192 onwards).
The neuron fires an action potential, no matter what value of current I inject into it. I suspect that stimulus is not working. Surprisingly, if I drop into Ipython shell during the execution (uncomment line no 205, and 205; when dropped into shell, type `exit` to return to normal execution), I see that changing properties of `IClamp` now changing the behavior of cell response: multiple fires for a small injected current, delayed stimulus causing delayed firing.
All files are kept at the following folder at github. They are many of them, running `test_nrn.sh` should reproduce the bug if any. The neuron I am using is compiled from source code.
https://github.com/BhallaLab/benchmarks ... models/bug
VERSION INFO ETC:
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NEURON -- VERSION 7.4 (1316:353c7c3ecd8d) 2015-04-03
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits
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Linux chamcham 3.13.0-40-generic #69-Ubuntu SMP Thu Nov 13 17:53:56 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux