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

Index of group ./specifications/pclamp

Index
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clamping parameters of a model to a (series of) predefined value(s)

this test also tests the output_filename command.
1. Commands to run the purkinje cell from an ndf file, voltage clamp
2. Commands to run the purkinje cell from an ndf file, current clamp

1. Commands to run the purkinje cell from an ndf file, voltage clamp

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 we find the input class template we would like to use ?





1. Executed command
list inputclass_templates




2. Expected output 
all input class templates:
  perfectclamp:
    module_name: Experiment
    options:
      command: command value
      name: name of this inputclass
    package: Experiment::PerfectClamp
  pulsegen:
    module_name: Experiment
    options:
      baselevel: The pulse base level
      delay1: First pulse delay
      delay2: Second pulse delay
      level1: First pulse level
      level2: Second pulse level
      name: name of this inputclass
      triggermode: 'The pulse triggermode, 0 - freerun, 1 - ext trig, 2 - ext gate'
      width1: First pulse width
      width2: Second pulse width
    package: Experiment::PulseGen








1.4. Can we create a voltage clamp circuitry object ?





1. Executed command
inputclass_add perfectclamp voltage_clamp_protocol name voltage_clamp_protocol command -0.060




2. Expected output 







1.5. Can we find the input class we just created ?





1. Executed command
list inputclasses




2. Expected output 
all input classes:
  voltage_clamp_protocol:
    module_name: Experiment
    options:
      command: -0.060
      name: voltage_clamp_protocol
    package: Experiment::PerfectClamp








1.6. Can we connect the voltage clamp circuitry to the purkinje cell soma ?





1. Executed command
input_add voltage_clamp_protocol /Purkinje/segments/soma Vm




2. Expected output 







1.7. Can we get information about the applied inputs ?





1. Executed command
input_show




2. Expected output 

- component_name: /Purkinje/segments/soma
  field: Vm
  inputclass: voltage_clamp_protocol








1.8. Can we add an output for /Purkinje/segments/soma->Vm ?





1. Executed command
output_add /Purkinje/segments/soma Vm




2. Expected output 







1.9. Can we add an output for /Purkinje/segments/b0s01[0]->Vm ?





1. Executed command
output_add /Purkinje/segments/b0s01[0] Vm




2. Expected output 







1.10. Can we add an output for /Purkinje/segments/b0s03[56]->Vm ?





1. Executed command
output_add /Purkinje/segments/b0s03[56] Vm




2. Expected output 







1.11. Can we add an output for /Purkinje/segments/b1s06[137]->Vm ?





1. Executed command
output_add /Purkinje/segments/b1s06[137] Vm




2. Expected output 







1.12. Can we add an output for /Purkinje/segments/b1s12[26]->Vm ?





1. Executed command
output_add /Purkinje/segments/b1s12[26] Vm




2. Expected output 







1.13. Can we add an output for /Purkinje/segments/b2s30[3]->Vm ?





1. Executed command
output_add /Purkinje/segments/b2s30[3] Vm




2. Expected output 







1.14. Can we add an output for /Purkinje/segments/b3s44[49]->Vm ?





1. Executed command
output_add /Purkinje/segments/b3s44[49] Vm




2. Expected output 







1.15. Can we set the output filename ?





1. Executed command
output_filename /tmp/pclamp.out




2. Expected output 







1.16. Can we check the simulation ?





1. Executed command
check /Purkinje




2. Expected output 







1.17. Can we run the simulation ?





1. Executed command
run /Purkinje 0.001




2. Expected output 







1.18. Can we find the output ?





1. Executed command
sh cat /tmp/pclamp.out




2. Expected output 
2e-05 -0.06 -0.0679887 -0.0680006 -0.067999 -0.0680012 -0.0679994 -0.0679984
4e-05 -0.06 -0.066381 -0.0679989 -0.0679982 -0.0680023 -0.0679986 -0.067997
6e-05 -0.06 -0.0650784 -0.0679867 -0.067997 -0.0680032 -0.0679976 -0.0679956
8e-05 -0.06 -0.0650376 -0.0679566 -0.0679943 -0.0680041 -0.0679966 -0.0679942
0.0001 -0.06 -0.0645753 -0.0679119 -0.0679892 -0.068005 -0.0679955 -0.0679928
0.00012 -0.06 -0.0645078 -0.0678612 -0.0679816 -0.0680058 -0.0679945 -0.0679915
0.00014 -0.06 -0.0643266 -0.0678092 -0.067972 -0.0680065 -0.0679934 -0.0679902
0.00016 -0.06 -0.0642346 -0.0677574 -0.0679609 -0.0680072 -0.0679924 -0.067989
0.00018 -0.06 -0.0641527 -0.0677072 -0.0679485 -0.0680078 -0.0679914 -0.0679877
0.0002 -0.06 -0.0640658 -0.0676588 -0.0679352 -0.0680084 -0.0679903 -0.0679865
0.00022 -0.06 -0.0640199 -0.0676123 -0.0679211 -0.0680089 -0.0679892 -0.0679853
0.00024 -0.06 -0.063947 -0.0675677 -0.0679064 -0.0680094 -0.0679881 -0.0679841
0.00026 -0.06 -0.0639146 -0.0675249 -0.0678911 -0.0680099 -0.067987 -0.0679829
0.00028 -0.06 -0.0638555 -0.0674837 -0.0678754 -0.0680102 -0.0679858 -0.0679817
0.0003 -0.06 -0.0638287 -0.067444 -0.0678594 -0.0680105 -0.0679846 -0.0679805
0.00032 -0.06 -0.0637805 -0.0674057 -0.0678431 -0.0680108 -0.0679833 -0.0679793
0.00034 -0.06 -0.0637566 -0.0673685 -0.0678265 -0.068011 -0.067982 -0.0679781
0.00036 -0.06 -0.0637166 -0.0673325 -0.0678097 -0.0680111 -0.0679807 -0.0679769
0.00038 -0.06 -0.0636945 -0.0672974 -0.0677929 -0.0680112 -0.0679793 -0.0679756
0.0004 -0.06 -0.0636605 -0.0672633 -0.0677759 -0.0680113 -0.0679779 -0.0679743
0.00042 -0.06 -0.0636399 -0.06723 -0.0677588 -0.0680112 -0.0679765 -0.067973
0.00044 -0.06 -0.0636104 -0.0671974 -0.0677417 -0.0680111 -0.0679751 -0.0679717
0.00046 -0.06 -0.063591 -0.0671655 -0.0677245 -0.068011 -0.0679736 -0.0679704
0.00048 -0.06 -0.063565 -0.0671343 -0.0677074 -0.0680108 -0.067972 -0.067969
0.0005 -0.06 -0.0635467 -0.0671037 -0.0676903 -0.0680105 -0.0679705 -0.0679677
0.00052 -0.06 -0.0635233 -0.0670736 -0.0676732 -0.0680102 -0.0679689 -0.0679663
0.00054 -0.06 -0.0635059 -0.067044 -0.0676562 -0.0680098 -0.0679673 -0.0679648
0.00056 -0.06 -0.0634847 -0.0670149 -0.0676392 -0.0680094 -0.0679657 -0.0679634
0.00058 -0.06 -0.0634682 -0.0669862 -0.0676223 -0.0680089 -0.067964 -0.067962
0.0006 -0.06 -0.0634487 -0.0669579 -0.0676055 -0.0680083 -0.0679623 -0.0679605
0.00062 -0.06 -0.063433 -0.0669301 -0.0675888 -0.0680077 -0.0679606 -0.067959
0.00064 -0.06 -0.063415 -0.0669026 -0.0675722 -0.0680071 -0.0679588 -0.0679574
0.00066 -0.06 -0.0634 -0.0668754 -0.0675556 -0.0680064 -0.0679571 -0.0679559
0.00068 -0.06 -0.0633832 -0.0668486 -0.0675392 -0.0680056 -0.0679553 -0.0679543
0.0007 -0.06 -0.0633688 -0.0668221 -0.067523 -0.0680048 -0.0679535 -0.0679527
0.00072 -0.06 -0.0633531 -0.0667959 -0.0675068 -0.0680039 -0.0679516 -0.0679511
0.00074 -0.06 -0.0633393 -0.06677 -0.0674908 -0.068003 -0.0679497 -0.0679495
0.00076 -0.06 -0.0633245 -0.0667444 -0.0674749 -0.068002 -0.0679479 -0.0679478
0.00078 -0.06 -0.0633113 -0.066719 -0.0674591 -0.0680009 -0.067946 -0.0679462
0.0008 -0.06 -0.0632972 -0.0666939 -0.0674434 -0.0679999 -0.067944 -0.0679444
0.00082 -0.06 -0.0632845 -0.066669 -0.0674279 -0.0679987 -0.0679421 -0.0679427
0.00084 -0.06 -0.0632712 -0.0666444 -0.0674125 -0.0679975 -0.0679401 -0.067941
0.00086 -0.06 -0.063259 -0.06662 -0.0673973 -0.0679963 -0.0679381 -0.0679392
0.00088 -0.06 -0.0632462 -0.0665958 -0.0673822 -0.067995 -0.0679361 -0.0679374
0.0009 -0.06 -0.0632344 -0.0665718 -0.0673672 -0.0679937 -0.0679341 -0.0679356
0.00092 -0.06 -0.0632222 -0.066548 -0.0673524 -0.0679923 -0.067932 -0.0679338
0.00094 -0.06 -0.0632109 -0.0665245 -0.0673377 -0.0679909 -0.06793 -0.0679319
0.00096 -0.06 -0.0631992 -0.0665011 -0.0673231 -0.0679894 -0.0679279 -0.06793
0.00098 -0.06 -0.0631882 -0.0664779 -0.0673087 -0.0679879 -0.0679258 -0.0679281
0.001 -0.06 -0.063177 -0.066455 -0.0672944 -0.0679863 -0.0679237 -0.0679262








2. Commands to run the purkinje cell from an ndf file, current clamp
Startup command : bin/genesis-g3
(No model has been loaded for the following set of commands.)
2.1. Is startup successful ?





1. Expected output 
GENESIS 3 shell







2.2. Can we load the purkinje cell model ?





1. Executed command
ndf_load cells/purkinje/edsjb1994.ndf




2. Expected output 







2.3. Can we find the input class template we would like to use ?





1. Executed command
list inputclass_templates




2. Expected output 
all input class templates:
  perfectclamp:
    module_name: Experiment
    options:
      command: command value
      name: name of this inputclass
    package: Experiment::PerfectClamp
  pulsegen:
    module_name: Experiment
    options:
      baselevel: The pulse base level
      delay1: First pulse delay
      delay2: Second pulse delay
      level1: First pulse level
      level2: Second pulse level
      name: name of this inputclass
      triggermode: 'The pulse triggermode, 0 - freerun, 1 - ext trig, 2 - ext gate'
      width1: First pulse width
      width2: Second pulse width
    package: Experiment::PulseGen








2.4. Can we create a current clamp circuitry object ?





1. Executed command
inputclass_add perfectclamp current_clamp_protocol name current_clamp_protocol command 1e-9




2. Expected output 







2.5. Can we find the input class we just created ?





1. Executed command
list inputclasses




2. Expected output 
all input classes:
  current_clamp_protocol:
    module_name: Experiment
    options:
      command: 1e-9
      name: current_clamp_protocol
    package: Experiment::PerfectClamp








2.6. Can we connect the current clamp circuitry to the purkinje cell soma ?





1. Executed command
input_add current_clamp_protocol /Purkinje/segments/soma INJECT




2. Expected output 







2.7. Can we get information about the applied inputs ?





1. Executed command
input_show




2. Expected output 

- component_name: /Purkinje/segments/soma
  field: INJECT
  inputclass: current_clamp_protocol








2.8. Can we add an output for /Purkinje/segments/soma->Vm ?





1. Executed command
output_add /Purkinje/segments/soma Vm




2. Expected output 







2.9. Can we add an output for /Purkinje/segments/b0s01[0]->Vm ?





1. Executed command
output_add /Purkinje/segments/b0s01[0] Vm




2. Expected output 







2.10. Can we add an output for /Purkinje/segments/b0s03[56]->Vm ?





1. Executed command
output_add /Purkinje/segments/b0s03[56] Vm




2. Expected output 







2.11. Can we add an output for /Purkinje/segments/b1s06[137]->Vm ?





1. Executed command
output_add /Purkinje/segments/b1s06[137] Vm




2. Expected output 







2.12. Can we add an output for /Purkinje/segments/b1s12[26]->Vm ?





1. Executed command
output_add /Purkinje/segments/b1s12[26] Vm




2. Expected output 







2.13. Can we add an output for /Purkinje/segments/b2s30[3]->Vm ?





1. Executed command
output_add /Purkinje/segments/b2s30[3] Vm




2. Expected output 







2.14. Can we add an output for /Purkinje/segments/b3s44[49]->Vm ?





1. Executed command
output_add /Purkinje/segments/b3s44[49] Vm




2. Expected output 







2.15. Can we set the output filename ?





1. Executed command
output_filename /tmp/pclamp.out




2. Expected output 







2.16. Can we check the simulation ?





1. Executed command
check /Purkinje




2. Expected output 







2.17. Can we run the simulation ?





1. Executed command
run /Purkinje 0.001




2. Expected output 







2.18. Can we find the output ?





1. Executed command
sh cat /tmp/pclamp.out




2. Expected output 
2e-05 -0.0679941 -0.0679887 -0.0680006 -0.067999 -0.0680012 -0.0679994 -0.0679984
4e-05 -0.0676033 -0.0679368 -0.068001 -0.0679983 -0.0680023 -0.0679986 -0.067997
6e-05 -0.0672794 -0.067818 -0.0680008 -0.0679976 -0.0680032 -0.0679976 -0.0679956
8e-05 -0.0669914 -0.0676855 -0.0679993 -0.0679968 -0.0680041 -0.0679966 -0.0679942
0.0001 -0.0667366 -0.0675582 -0.067996 -0.067996 -0.068005 -0.0679955 -0.0679928
0.00012 -0.066506 -0.0674328 -0.0679907 -0.0679948 -0.0680058 -0.0679945 -0.0679915
0.00014 -0.0662975 -0.0673156 -0.0679835 -0.0679934 -0.0680065 -0.0679935 -0.0679902
0.00016 -0.0661071 -0.0672035 -0.0679745 -0.0679915 -0.0680072 -0.0679925 -0.067989
0.00018 -0.065933 -0.0670985 -0.0679641 -0.0679893 -0.0680078 -0.0679915 -0.0679878
0.0002 -0.0657728 -0.0669991 -0.0679524 -0.0679866 -0.0680084 -0.0679905 -0.0679866
0.00022 -0.0656251 -0.0669055 -0.0679397 -0.0679835 -0.068009 -0.0679895 -0.0679854
0.00024 -0.0654885 -0.0668173 -0.0679261 -0.06798 -0.0680095 -0.0679886 -0.0679843
0.00026 -0.0653617 -0.0667339 -0.0679117 -0.0679762 -0.06801 -0.0679876 -0.0679832
0.00028 -0.0652438 -0.0666552 -0.0678968 -0.0679719 -0.0680104 -0.0679866 -0.0679821
0.0003 -0.0651339 -0.0665806 -0.0678814 -0.0679673 -0.0680108 -0.0679857 -0.067981
0.00032 -0.0650312 -0.0665101 -0.0678656 -0.0679624 -0.0680112 -0.0679847 -0.06798
0.00034 -0.0649351 -0.0664431 -0.0678495 -0.0679571 -0.0680115 -0.0679837 -0.0679789
0.00036 -0.0648448 -0.0663796 -0.0678331 -0.0679515 -0.0680118 -0.0679827 -0.0679778
0.00038 -0.06476 -0.066319 -0.0678166 -0.0679456 -0.0680121 -0.0679817 -0.0679768
0.0004 -0.0646801 -0.0662615 -0.0677998 -0.0679395 -0.0680123 -0.0679806 -0.0679758
0.00042 -0.0646048 -0.0662065 -0.067783 -0.0679331 -0.0680125 -0.0679796 -0.0679747
0.00044 -0.0645336 -0.0661542 -0.067766 -0.0679265 -0.0680127 -0.0679786 -0.0679737
0.00046 -0.0644661 -0.066104 -0.067749 -0.0679196 -0.0680128 -0.0679775 -0.0679726
0.00048 -0.0644022 -0.0660561 -0.0677319 -0.0679126 -0.0680129 -0.0679764 -0.0679716
0.0005 -0.0643415 -0.0660101 -0.0677148 -0.0679053 -0.068013 -0.0679753 -0.0679706
0.00052 -0.0642837 -0.065966 -0.0676977 -0.0678979 -0.068013 -0.0679742 -0.0679695
0.00054 -0.0642286 -0.0659235 -0.0676806 -0.0678903 -0.068013 -0.0679731 -0.0679685
0.00056 -0.0641761 -0.0658828 -0.0676635 -0.0678825 -0.068013 -0.0679719 -0.0679675
0.00058 -0.064126 -0.0658435 -0.0676464 -0.0678747 -0.068013 -0.0679708 -0.0679664
0.0006 -0.064078 -0.0658056 -0.0676293 -0.0678667 -0.0680129 -0.0679696 -0.0679654
0.00062 -0.064032 -0.0657691 -0.0676122 -0.0678585 -0.0680128 -0.0679684 -0.0679643
0.00064 -0.0639879 -0.0657338 -0.0675952 -0.0678503 -0.0680126 -0.0679672 -0.0679632
0.00066 -0.0639455 -0.0656996 -0.0675783 -0.067842 -0.0680124 -0.067966 -0.0679622
0.00068 -0.0639048 -0.0656665 -0.0675613 -0.0678336 -0.0680122 -0.0679648 -0.0679611
0.0007 -0.0638656 -0.0656345 -0.0675445 -0.0678251 -0.068012 -0.0679636 -0.06796
0.00072 -0.0638278 -0.0656034 -0.0675276 -0.0678165 -0.0680117 -0.0679623 -0.0679589
0.00074 -0.0637913 -0.0655732 -0.0675108 -0.0678079 -0.0680114 -0.0679611 -0.0679578
0.00076 -0.0637561 -0.0655439 -0.0674941 -0.0677992 -0.0680111 -0.0679598 -0.0679567
0.00078 -0.063722 -0.0655153 -0.0674774 -0.0677905 -0.0680107 -0.0679585 -0.0679556
0.0008 -0.0636891 -0.0654876 -0.0674608 -0.0677817 -0.0680103 -0.0679572 -0.0679545
0.00082 -0.0636571 -0.0654605 -0.0674442 -0.0677729 -0.0680099 -0.0679559 -0.0679534
0.00084 -0.0636262 -0.0654341 -0.0674277 -0.067764 -0.0680095 -0.0679546 -0.0679523
0.00086 -0.0635961 -0.0654084 -0.0674112 -0.0677552 -0.068009 -0.0679532 -0.0679511
0.00088 -0.0635669 -0.0653833 -0.0673947 -0.0677463 -0.0680085 -0.0679519 -0.06795
0.0009 -0.0635385 -0.0653587 -0.0673784 -0.0677373 -0.068008 -0.0679505 -0.0679488
0.00092 -0.0635108 -0.0653348 -0.067362 -0.0677284 -0.0680074 -0.0679492 -0.0679476
0.00094 -0.0634839 -0.0653113 -0.0673458 -0.0677195 -0.0680068 -0.0679478 -0.0679464
0.00096 -0.0634577 -0.0652883 -0.0673296 -0.0677105 -0.0680062 -0.0679464 -0.0679452
0.00098 -0.0634321 -0.0652658 -0.0673134 -0.0677016 -0.0680055 -0.067945 -0.067944
0.001 -0.0634071 -0.0652438 -0.0672973 -0.0676926 -0.0680049 -0.0679436 -0.0679428





3. Comment
This is supposed to produce the same as /usr/local/ssp/tests/specifications/strings/purkinje/builtin-edsjb1994-soma-current.txt, but it is slightly different