Lab notebook: : 20120919-154600

Label	20120919-154600
Motivation	Run script with AdExpIF instead of IF_BG4
Outcome	Runs much more slowly. Mean firing rates slightly higher (33 Hz for RS) than in previous simulation (29 Hz). Differences seem to be due to behaviour around threshold: Vm170 data: t adexp IF_BG4 6.3 -52.7427 -52.7427 6.4 -51.9997 -51.9997 6.5 -51.2844 -51.2844 6.6 -50.595 -50.595 6.7 40 -49.9297 6.8 -60 39.0982 6.9 -60 -59.0093 7 -60 -59.9719
Date	19/09/2012
Time	15:46:00
Duration	233.55 s
Launch mode	serial

Code

Executable	Repository	Version	Main file	Arguments
Python 2.7.1 (/home/andrew/env/pyNN-0.7/bin/python)	https://bitbucket.org/apdavison/destexhe_jcns_2009	f6258f1f86d9	demo_cx05_N=500b_LTS.py

Dependencies

Name	Path	Version
distutils	/home/andrew/env/pyNN-0.7/lib/python2.7/distutils	2.7.1
encodings	/home/andrew/env/pyNN-0.7/lib/python2.7/encodings	unknown
neuron	/home/andrew/env/pyNN-0.7/lib/python2.7/site-packages/neuron	unknown
nose	/usr/lib/pymodules/python2.7/nose	0.11.4
numpy	/usr/lib/pymodules/python2.7/numpy	1.5.1
pyNN	/home/andrew/env/pyNN-0.7/lib/python2.7/site-packages/pyNN	1214
scipy	/usr/lib/python2.7/dist-packages/scipy	0.8.0

Inputs

Outputs

Output files

/home/docker/site
20120919-154600/Vm170_cx05_LTS500b.dat	08200b874c4bdad5b877cea0534dd5b0c98f4b0c	text/plain	740.3 KB
20120919-154600/numspikes_cx05_LTS500b.dat	7838b81ee18d1c9a637d9e5d1caf2b08676240ec	text/plain	1.7 KB
20120919-154600/spiketimes_cx05_LTS500b.dat	aa0012449fa46f96953b586fae3ffdc298ec9710	text/plain	845.7 KB

Stdout & Stderr

MPI_Initialized==false, disabling MPI functionality.
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

loading membrane mechanisms from x86_64/.libs/libnrnmech.so
Additional mechanisms from files
 gen5.mod multiAMPAexp.mod multiGABAAexp.mod multiStimexp.mod
NEURON: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed"
	1 
loading membrane mechanisms from /home/andrew/env/pyNN-0.7/lib/python2.7/site-packages/pyNN/neuron/nmodl/x86_64/.libs/libnrnmech.so
Additional mechanisms from files
 adexp.mod alphaisyn.mod alphasyn.mod expisyn.mod gsfa_grr.mod hh_traub.mod netstim2.mod refrac.mod reset.mod stdwa_guetig.mod stdwa_softlimits.mod stdwa_songabbott.mod stdwa_symm.mod tmgsyn.mod tmisyn.mod vecstim.mod

=======================================================================
            Network of  500 IF neurons in an active state
=======================================================================

----[ CREATING CELLS ]----
Cell  116  is LTS
Cell  156  is LTS
Cell  167  is LTS
Cell  207  is LTS
Cell  228  is LTS
Cell  238  is LTS
Cell  243  is LTS
Cell  254  is LTS
Cell  299  is LTS
Cell  341  is LTS
Cell  352  is LTS
Cell  387  is LTS
Cell  399  is LTS
----[ CREATING NETWORK ]----
Calculate connectivity of cortical cells...
MEAN SYNAPSES PER NEURON:
cortical excitatory inputs  29.95
cortical inhibitory inputs  6.934
----[ ADDING NETWORK INPUT ]----
Add stimulation of cortical neurons...
>>> Writing spikes on file...
Mean rate per RS cell (Hz) =  33.216
 standard deviation =  29.4361978523
Mean rate per FS cell (Hz) =  35.826
 standard deviation =  32.0133179161
>>> 
Exception in thread Thread-1 (most likely raised during interpreter shutdown):
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 552, in __bootstrap_inner
  File "/home/andrew/env/pyNN-0.7/lib/python2.7/site-packages/neuron/gui.py", line 36, in run
  File "/home/andrew/env/pyNN-0.7/lib/python2.7/site-packages/neuron/gui.py", line 17, in process_events
<type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'doNotify'

Environment

Name	IP address	Processor	Architecture		System type	Release	Version
retina	127.0.1.1	x86_64 x86_64	64bit	ELF	Linux	2.6.38-11-generic	#50-Ubuntu SMP Mon Sep 12 21:17:25 UTC 2011