Main Neurospaces logo neurospaces 0.1675 Thu, 27 Dec 2007 15:58:18 -0600 hugo

Index of group ./specifications/single_synapse

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single synaptic stimulation simulations

1. Commands to run the purkinje cell from an ndf file, single synaptic stimulation
2. Running the purkinje cell with single synaptic stimulation from a G3 batch file
3. Running the purkinje cell with single synaptic stimulation from a perl script

1. Commands to run the purkinje cell from an ndf file, single synaptic stimulation

Startup command : bin/genesis-g3

(No model has been loaded for the following set of commands.)

1.1. Is startup successful ?

1. Expected output 
GENESIS 3 shell

1.2. Can we load the purkinje cell model ?

1. Executed command
ndf_load cells/purkinje/edsjb1994.ndf
2. Expected output 







1.3. Can prepare the morphology of a structural analysis ?





1. Executed command
morphology_summarize /Purkinje




2. Expected output 

---
Number of segments: 4548
Number of segments without parents: 1
Number of segment tips: 1474








1.4. Can we get information about the number of branch points for a chosen dendritic segment ?





1. Executed command
parameter_show /Purkinje/segments/b1s06[182] SOMATOPETAL_BRANCHPOINTS




2. Expected output 
value = 23







1.5. Can we attach an event list to this dendritic segment ?





1. Executed command
runtime_parameter_add /Purkinje/segments/b1s06[182]/Purkinje_spine_0/head/par/synapse EVENT_FILENAME event_data/events.yml




2. Expected output 







1.6. Can we check the simulation ?





1. Executed command
check /Purkinje




2. Expected output 







1.7. Can we run the simulation ?





1. Executed command
run /Purkinje 0.001




2. Expected output 







1.8. Can we find the output ?





1. Executed command
sh cat /tmp/output




2. Expected output 

0.001 -0.0587013








2. Running the purkinje cell with single synaptic stimulation from a G3 batch file
Startup command : bin/genesis-g3 ./..//tests/scripts/simple_purkinje.g3
2.1. Can we run the purkinje cell with single synaptic stimulation from a G3 batch file ?





1. Expected output 
loading purkinje cell
loaded
applying current injection
running for 0.001sec
output follows:
2e-05 -0.0672264
4e-05 -0.0665857
6e-05 -0.0660166
8e-05 -0.0655132
0.0001 -0.065058
0.00012 -0.0646468
0.00014 -0.0642712
0.00016 -0.0639279
0.00018 -0.063612
0.0002 -0.0633209
0.00022 -0.0630513
0.00024 -0.0628012
0.00026 -0.0625685
0.00028 -0.0623513
0.0003 -0.0621481
0.00032 -0.0619575
0.00034 -0.0617785
0.00036 -0.0616098
0.00038 -0.0614506
0.0004 -0.0612999
0.00042 -0.0611572
0.00044 -0.0610216
0.00046 -0.0608925
0.00048 -0.0607695
0.0005 -0.060652
0.00052 -0.0605396
0.00054 -0.0604319
0.00056 -0.0603285
0.00058 -0.060229
0.0006 -0.0601333
0.00062 -0.0600409
0.00064 -0.0599517
0.00066 -0.0598655
0.00068 -0.059782
0.0007 -0.059701
0.00072 -0.0596224
0.00074 -0.0595461
0.00076 -0.0594717
0.00078 -0.0593993
0.0008 -0.0593287
0.00082 -0.0592598
0.00084 -0.0591925
0.00086 -0.0591267
0.00088 -0.0590623
0.0009 -0.0589992
0.00092 -0.0589374
0.00094 -0.0588767
0.00096 -0.0588172
0.00098 -0.0587587
0.001 -0.0587013








3. Running the purkinje cell with single synaptic stimulation from a perl script
Startup command : ./..//tests/scripts/simple_purkinje
(No model has been loaded for the following set of commands.)
3.1. Can we run the purkinje cell with single synaptic stimulation from a perl script ?





1. Expected output 
loading purkinje cell
loaded
applying current injection
running for 0.001sec
output follows:
2e-05 -0.0672264
4e-05 -0.0665857
6e-05 -0.0660166
8e-05 -0.0655132
0.0001 -0.065058
0.00012 -0.0646468
0.00014 -0.0642712
0.00016 -0.0639279
0.00018 -0.063612
0.0002 -0.0633209
0.00022 -0.0630513
0.00024 -0.0628012
0.00026 -0.0625685
0.00028 -0.0623513
0.0003 -0.0621481
0.00032 -0.0619575
0.00034 -0.0617785
0.00036 -0.0616098
0.00038 -0.0614506
0.0004 -0.0612999
0.00042 -0.0611572
0.00044 -0.0610216
0.00046 -0.0608925
0.00048 -0.0607695
0.0005 -0.060652
0.00052 -0.0605396
0.00054 -0.0604319
0.00056 -0.0603285
0.00058 -0.060229
0.0006 -0.0601333
0.00062 -0.0600409
0.00064 -0.0599517
0.00066 -0.0598655
0.00068 -0.059782
0.0007 -0.059701
0.00072 -0.0596224
0.00074 -0.0595461
0.00076 -0.0594717
0.00078 -0.0593993
0.0008 -0.0593287
0.00082 -0.0592598
0.00084 -0.0591925
0.00086 -0.0591267
0.00088 -0.0590623
0.0009 -0.0589992
0.00092 -0.0589374
0.00094 -0.0588767
0.00096 -0.0588172
0.00098 -0.0587587
0.001 -0.0587013