Index of group ./specifications/builtins/cell

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cell builtin schedule

1. Schedule construction of a single neuron model from the cell builtin schedule
2. Schedule construction of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection
3. Schedule construction of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection specified as a parameter
4. Schedule construction of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection with set duration and simulation time
5. Simulation of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection with set duration and simulation time
6. Method history of a simulation of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection with set duration and simulation time
7. Simulation of a single neuron model from the cell builtin schedule, debug option turned on
8. Invocation of the neurospaces studio when using the cell builtin

1. Schedule construction of a single neuron model from the cell builtin schedule

Startup command : ./bin/ssp --cell cells/stand_alone.ndf --emit-schedules

1.1. Can we construct a schedule of a single neuron model from the cell builtin schedule ?

1. Expected output 

analyzers: \{\}
application_classes:
  analyzers:
    default:
      - method: analyze
    priority: 95
  finishers:
    default:
      - method: finish
    priority: 140
  initializers:
    default:
      - method: compile
      - method: connect
      - method: instantiate_inputs
      - method: instantiate_outputs
      - method: initiate
      - method: optimize
    priority: 80
  modifiers:
    default: \[\]
    priority: 50
  results:
    default: \[\]
    priority: 170
  services:
    default:
      - method: instantiate_services
    priority: 20
  simulation:
    default: \[\]
    priority: 110
apply:
  simulation:
    - arguments:
        - 0.05
        - verbose: 0
      method: advance
models:
  - granular_parameters: \[\]
    modelname: /stand_alone
    solverclass: heccer
name: 'builtin cell configuration, applied to: stand_alone'
outputclasses:
  double_2_ascii:
    module_name: Heccer
    options:
      filename: ./output/stand_alone\.out
    package: Heccer::Output
outputs:
  - component_name: /stand_alone/segments/soma
    field: Vm
    outputclass: double_2_ascii
services:
  model_container:
    initializers:
      - arguments:
          -
            - (.*?)/bin/ssp
            - -P
            - cells/stand_alone.ndf
        method: read
    model_library: /usr/local/neurospaces/models/library
    module_name: Neurospaces
solverclasses:
  heccer:
    module_name: Heccer
    service_name: model_container

2. Schedule construction of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection

Startup command : ./bin/ssp --cell cells/stand_alone.ndf --inject-magnitude 2e-8 --emit-schedules --output /stand_alone/segments/soma->Vm

2.1. Can we construct a schedule of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection ?

1. Expected output 

analyzers: \{\}
application_classes:
  analyzers:
    default:
      - method: analyze
    priority: 95
  finishers:
    default:
      - method: finish
    priority: 140
  initializers:
    default:
      - method: compile
      - method: connect
      - method: instantiate_inputs
      - method: instantiate_outputs
      - method: initiate
      - method: optimize
    priority: 80
  modifiers:
    default: \[\]
    priority: 50
  results:
    default: \[\]
    priority: 170
  services:
    default:
      - method: instantiate_services
    priority: 20
  simulation:
    default: \[\]
    priority: 110
apply:
  simulation:
    - arguments:
        - 0.05
        - verbose: 0
      method: advance
models:
  - granular_parameters:
      - component_name: /stand_alone/segments/soma
        field: INJECT
        value: 2e-8
        warn_only: 'the component_name is a default, its address may be wrong'
      - component_name: /stand_alone/soma
        field: INJECT
        value: 2e-8
        warn_only: 'the component_name is a default, its address may be wrong'
    modelname: /stand_alone
    solverclass: heccer
name: 'builtin cell configuration, applied to: stand_alone'
outputclasses:
  double_2_ascii:
    module_name: Heccer
    options:
      filename: ./output/stand_alone\.out
    package: Heccer::Output
outputs:
  - component_name: /stand_alone/segments/soma
    field: Vm
    outputclass: double_2_ascii
services:
  model_container:
    initializers:
      - arguments:
          -
            - (.*?)/bin/ssp
            - -P
            - cells/stand_alone.ndf
        method: read
    model_library: /usr/local/neurospaces/models/library
    module_name: Neurospaces
solverclasses:
  heccer:
    module_name: Heccer
    service_name: model_container

3. Schedule construction of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection specified as a parameter

Startup command : ./bin/ssp --cell cells/stand_alone.ndf --parameter /stand_alone/segments/soma->INJECT=2e-8 --emit-schedules --output /stand_alone/segments/soma->Vm

3.1. Can we construct a schedule of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection specified as a parameter ?

1. Expected output 

analyzers: \{\}
application_classes:
  analyzers:
    default:
      - method: analyze
    priority: 95
  finishers:
    default:
      - method: finish
    priority: 140
  initializers:
    default:
      - method: compile
      - method: connect
      - method: instantiate_inputs
      - method: instantiate_outputs
      - method: initiate
      - method: optimize
    priority: 80
  modifiers:
    default: \[\]
    priority: 50
  results:
    default: \[\]
    priority: 170
  services:
    default:
      - method: instantiate_services
    priority: 20
  simulation:
    default: \[\]
    priority: 110
apply:
  simulation:
    - arguments:
        - 0.05
        - verbose: 0
      method: advance
models:
  - granular_parameters:
      - component_name: /stand_alone/segments/soma
        field: INJECT
        value: 2e-8
    modelname: /stand_alone
    solverclass: heccer
name: 'builtin cell configuration, applied to: stand_alone'
outputclasses:
  double_2_ascii:
    module_name: Heccer
    options:
      filename: ./output/stand_alone\.out
    package: Heccer::Output
outputs:
  - component_name: /stand_alone/segments/soma
    field: Vm
    outputclass: double_2_ascii
services:
  model_container:
    initializers:
      - arguments:
          -
            - (.*?)/bin/ssp
            - -P
            - cells/stand_alone.ndf
        method: read
    model_library: /usr/local/neurospaces/models/library
    module_name: Neurospaces
solverclasses:
  heccer:
    module_name: Heccer
    service_name: model_container

4. Schedule construction of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection with set duration and simulation time

Startup command : ./bin/ssp --cell cells/stand_alone.ndf --inject-magnitude 2e-8 --inject-delay 0.01 --inject-duration 0.03 --time 0.06 --emit-schedules --output /stand_alone/segments/soma->Vm

4.1. Can we construct a schedule of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection with set duration and simulation time ?

1. Expected output 

analyzers: \{\}
application_classes:
  analyzers:
    default:
      - method: analyze
    priority: 95
  finishers:
    default:
      - method: finish
    priority: 140
  initializers:
    default:
      - method: compile
      - method: connect
      - method: instantiate_inputs
      - method: instantiate_outputs
      - method: initiate
      - method: optimize
    priority: 80
  modifiers:
    default: \[\]
    priority: 50
  results:
    default: \[\]
    priority: 170
  services:
    default:
      - method: instantiate_services
    priority: 20
  simulation:
    default: \[\]
    priority: 110
apply:
  simulation:
    - arguments:
        - 0.01
        - verbose: 0
      method: advance
    - arguments:
        - component_name: /stand_alone/segments/soma
          field: INJECT
          modelname: /stand_alone
          value: 2e-8
      method: apply_runtime_parameters
    - arguments:
        - 0.03
        - verbose: 0
      method: advance
    - arguments:
        - component_name: /stand_alone/segments/soma
          field: INJECT
          modelname: /stand_alone
          value: 0
      method: apply_runtime_parameters
    - arguments:
        - 0.02
        - verbose: 0
      method: advance
models:
  - granular_parameters: \[\]
    modelname: /stand_alone
    solverclass: heccer
name: 'builtin cell configuration, applied to: stand_alone'
outputclasses:
  double_2_ascii:
    module_name: Heccer
    options:
      filename: ./output/stand_alone\.out
    package: Heccer::Output
outputs:
  - component_name: /stand_alone/segments/soma
    field: Vm
    outputclass: double_2_ascii
services:
  model_container:
    initializers:
      - arguments:
          -
            - (.*?)/bin/ssp
            - -P
            - cells/stand_alone.ndf
        method: read
    model_library: /usr/local/neurospaces/models/library
    module_name: Neurospaces
solverclasses:
  heccer:
    module_name: Heccer
    service_name: model_container

5. Simulation of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection with set duration and simulation time

Startup command : ./bin/ssp --cell cells/stand_alone.ndf --inject-magnitude 2e-8 --inject-delay 0.01 --inject-duration 0.03 --time 0.06 --output /stand_alone/segments/soma->Vm --emit-output output/stand_alone.out

Comments, Preparation, Reparation

1. Preparation needed before the commands below : 
No preparation necessary
2. And repared afterwards using : 
Removing the output from the distribution, needed for distcheck to work properly

5.1. Can we run a schedule of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection with set duration and simulation time ?

1. Expected output 
2e-05 -0.0700242
4e-05 -0.0700481
6e-05 -0.0700716
8e-05 -0.0700949
0.0001 -0.0701178
0.00012 -0.0701404
0.00014 -0.0701628
0.00016 -0.0701848
0.00018 -0.0702065
0.0002 -0.0702279
0.00022 -0.070249
0.00024 -0.0702698
0.00026 -0.0702903
0.00028 -0.0703105
0.0003 -0.0703305
0.00032 -0.0703502
0.00034 -0.0703695
0.00036 -0.0703886
0.00038 -0.0704074
0.0004 -0.070426
0.00042 -0.0704443
0.00044 -0.0704623
0.00046 -0.07048
0.00048 -0.0704975
0.0005 -0.0705147
0.00052 -0.0705317
0.00054 -0.0705484
0.00056 -0.0705649
0.00058 -0.0705811
0.0006 -0.0705971
0.00062 -0.0706128
0.00064 -0.0706283
0.00066 -0.0706435
0.00068 -0.0706585
0.0007 -0.0706733
0.00072 -0.0706878
0.00074 -0.0707021
0.00076 -0.0707162
0.00078 -0.07073
0.0008 -0.0707437
0.00082 -0.0707571
0.00084 -0.0707703
0.00086 -0.0707833
0.00088 -0.070796
0.0009 -0.0708086
0.00092 -0.070821
0.00094 -0.0708331
0.00096 -0.070845
0.00098 -0.0708568
0.001 -0.0708683
0.00102 -0.0708797
0.00104 -0.0708908
0.00106 -0.0709018
0.00108 -0.0709126
0.0011 -0.0709231
0.00112 -0.0709335
0.00114 -0.0709438
0.00116 -0.0709538
0.00118 -0.0709636
0.0012 -0.0709733
0.00122 -0.0709828
0.00124 -0.0709922
0.00126 -0.0710013
0.00128 -0.0710103
0.0013 -0.0710191
0.00132 -0.0710278
0.00134 -0.0710363
0.00136 -0.0710446
0.00138 -0.0710528
0.0014 -0.0710608
0.00142 -0.0710687
0.00144 -0.0710764
0.00146 -0.0710839
0.00148 -0.0710913
0.0015 -0.0710986
0.00152 -0.0711057
0.00154 -0.0711127
0.00156 -0.0711195
0.00158 -0.0711262
0.0016 -0.0711328
0.00162 -0.0711392
0.00164 -0.0711455
0.00166 -0.0711516
0.00168 -0.0711576
0.0017 -0.0711635
0.00172 -0.0711693
0.00174 -0.0711749
0.00176 -0.0711804
0.00178 -0.0711858
0.0018 -0.071191
0.00182 -0.0711962
0.00184 -0.0712012
0.00186 -0.0712061
0.00188 -0.0712109
0.0019 -0.0712155
0.00192 -0.0712201
0.00194 -0.0712245
0.00196 -0.0712289
0.00198 -0.0712331
0.002 -0.0712372
0.00202 -0.0712412
0.00204 -0.0712451
0.00206 -0.0712489
0.00208 -0.0712526
0.0021 -0.0712562
0.00212 -0.0712598
0.00214 -0.0712632
0.00216 -0.0712665
0.00218 -0.0712697
0.0022 -0.0712728
0.00222 -0.0712759
0.00224 -0.0712788
0.00226 -0.0712816
0.00228 -0.0712844
0.0023 -0.0712871
0.00232 -0.0712897
0.00234 -0.0712922
0.00236 -0.0712946
0.00238 -0.071297
0.0024 -0.0712992
0.00242 -0.0713014
0.00244 -0.0713035
0.00246 -0.0713055
0.00248 -0.0713075
0.0025 -0.0713094
0.00252 -0.0713112
0.00254 -0.0713129
0.00256 -0.0713145
0.00258 -0.0713161
0.0026 -0.0713176
0.00262 -0.0713191
0.00264 -0.0713204
0.00266 -0.0713217
0.00268 -0.071323
0.0027 -0.0713241
0.00272 -0.0713253
0.00274 -0.0713263
0.00276 -0.0713273
0.00278 -0.0713282
0.0028 -0.0713291
0.00282 -0.0713299
0.00284 -0.0713306
0.00286 -0.0713313
0.00288 -0.0713319
0.0029 -0.0713325
0.00292 -0.071333
0.00294 -0.0713335
0.00296 -0.0713339
0.00298 -0.0713343
0.003 -0.0713346
0.00302 -0.0713349
0.00304 -0.0713351
0.00306 -0.0713352
0.00308 -0.0713354
0.0031 -0.0713354
0.00312 -0.0713355
0.00314 -0.0713354
0.00316 -0.0713354
0.00318 -0.0713353
0.0032 -0.0713351
0.00322 -0.0713349
0.00324 -0.0713347
0.00326 -0.0713344
0.00328 -0.0713341
0.0033 -0.0713337
0.00332 -0.0713334
0.00334 -0.0713329
0.00336 -0.0713324
0.00338 -0.0713319
0.0034 -0.0713314
0.00342 -0.0713308
0.00344 -0.0713302
0.00346 -0.0713296
0.00348 -0.0713289
0.0035 -0.0713282
0.00352 -0.0713274
0.00354 -0.0713266
0.00356 -0.0713258
0.00358 -0.071325
0.0036 -0.0713241
0.00362 -0.0713232
0.00364 -0.0713223
0.00366 -0.0713213
0.00368 -0.0713203
0.0037 -0.0713193
0.00372 -0.0713183
0.00374 -0.0713172
0.00376 -0.0713161
0.00378 -0.071315
0.0038 -0.0713138
0.00382 -0.0713126
0.00384 -0.0713114
0.00386 -0.0713102
0.00388 -0.071309
0.0039 -0.0713077
0.00392 -0.0713064
0.00394 -0.0713051
0.00396 -0.0713038
0.00398 -0.0713024
0.004 -0.071301
0.00402 -0.0712996
0.00404 -0.0712982
0.00406 -0.0712968
0.00408 -0.0712953
0.0041 -0.0712939
0.00412 -0.0712924
0.00414 -0.0712909
0.00416 -0.0712894
0.00418 -0.0712878
0.0042 -0.0712863
0.00422 -0.0712847
0.00424 -0.0712831
0.00426 -0.0712816
0.00428 -0.0712799
0.0043 -0.0712783
0.00432 -0.0712767
0.00434 -0.0712751
0.00436 -0.0712734
0.00438 -0.0712717
0.0044 -0.0712701
0.00442 -0.0712684
0.00444 -0.0712667
0.00446 -0.0712649
0.00448 -0.0712632
0.0045 -0.0712615
0.00452 -0.0712597
0.00454 -0.071258
0.00456 -0.0712562
0.00458 -0.0712544
0.0046 -0.0712526
0.00462 -0.0712508
0.00464 -0.071249
0.00466 -0.0712472
0.00468 -0.0712454
0.0047 -0.0712436
0.00472 -0.0712418
0.00474 -0.0712399
0.00476 -0.0712381
0.00478 -0.0712362
0.0048 -0.0712344
0.00482 -0.0712325
0.00484 -0.0712307
0.00486 -0.0712288
0.00488 -0.0712269
0.0049 -0.071225
0.00492 -0.0712232
0.00494 -0.0712213
0.00496 -0.0712194
0.00498 -0.0712175
0.005 -0.0712156
0.00502 -0.0712137
0.00504 -0.0712118
0.00506 -0.0712099
0.00508 -0.071208
0.0051 -0.0712061
0.00512 -0.0712041
0.00514 -0.0712022
0.00516 -0.0712003
0.00518 -0.0711984
0.0052 -0.0711964
0.00522 -0.0711945
0.00524 -0.0711926
0.00526 -0.0711907
0.00528 -0.0711888
0.0053 -0.0711868
0.00532 -0.0711849
0.00534 -0.071183
0.00536 -0.0711811
0.00538 -0.0711791
0.0054 -0.0711772
0.00542 -0.0711753
0.00544 -0.0711734
0.00546 -0.0711715
0.00548 -0.0711696
0.0055 -0.0711676
0.00552 -0.0711657
0.00554 -0.0711638
0.00556 -0.0711619
0.00558 -0.07116
0.0056 -0.0711581
0.00562 -0.0711562
0.00564 -0.0711543
0.00566 -0.0711524
0.00568 -0.0711505
0.0057 -0.0711486
0.00572 -0.0711467
0.00574 -0.0711448
0.00576 -0.0711429
0.00578 -0.071141
0.0058 -0.0711391
0.00582 -0.0711373
0.00584 -0.0711354
0.00586 -0.0711335
0.00588 -0.0711317
0.0059 -0.0711298
0.00592 -0.0711279
0.00594 -0.0711261
0.00596 -0.0711243
0.00598 -0.0711224
0.006 -0.0711206
0.00602 -0.0711187
0.00604 -0.0711169
0.00606 -0.0711151
0.00608 -0.0711133
0.0061 -0.0711115
0.00612 -0.0711097
0.00614 -0.0711079
0.00616 -0.0711061
0.00618 -0.0711043
0.0062 -0.0711025
0.00622 -0.0711007
0.00624 -0.0710989
0.00626 -0.0710971
0.00628 -0.0710953
0.0063 -0.0710936
0.00632 -0.0710918
0.00634 -0.0710901
0.00636 -0.0710883
0.00638 -0.0710866
0.0064 -0.0710849
0.00642 -0.0710832
0.00644 -0.0710814
0.00646 -0.0710797
0.00648 -0.071078
0.0065 -0.0710763
0.00652 -0.0710746
0.00654 -0.071073
0.00656 -0.0710713
0.00658 -0.0710696
0.0066 -0.071068
0.00662 -0.0710663
0.00664 -0.0710646
0.00666 -0.071063
0.00668 -0.0710614
0.0067 -0.0710597
0.00672 -0.0710581
0.00674 -0.0710565
0.00676 -0.0710549
0.00678 -0.0710533
0.0068 -0.0710517
0.00682 -0.0710501
0.00684 -0.0710485
0.00686 -0.0710469
0.00688 -0.0710453
0.0069 -0.0710438
0.00692 -0.0710422
0.00694 -0.0710407
0.00696 -0.0710391
0.00698 -0.0710376
0.007 -0.0710361
0.00702 -0.0710345
0.00704 -0.071033
0.00706 -0.0710315
0.00708 -0.07103
0.0071 -0.0710286
0.00712 -0.0710271
0.00714 -0.0710256
0.00716 -0.0710241
0.00718 -0.0710227
0.0072 -0.0710212
0.00722 -0.0710198
0.00724 -0.0710184
0.00726 -0.0710169
0.00728 -0.0710155
0.0073 -0.0710141
0.00732 -0.0710127
0.00734 -0.0710113
0.00736 -0.0710099
0.00738 -0.0710085
0.0074 -0.0710072
0.00742 -0.0710058
0.00744 -0.0710044
0.00746 -0.0710031
0.00748 -0.0710017
0.0075 -0.0710004
0.00752 -0.0709991
0.00754 -0.0709977
0.00756 -0.0709964
0.00758 -0.0709951
0.0076 -0.0709938
0.00762 -0.0709925
0.00764 -0.0709912
0.00766 -0.07099
0.00768 -0.0709887
0.0077 -0.0709874
0.00772 -0.0709862
0.00774 -0.0709849
0.00776 -0.0709837
0.00778 -0.0709825
0.0078 -0.0709813
0.00782 -0.0709801
0.00784 -0.0709789
0.00786 -0.0709777
0.00788 -0.0709765
0.0079 -0.0709753
0.00792 -0.0709741
0.00794 -0.070973
0.00796 -0.0709718
0.00798 -0.0709707
0.008 -0.0709695
0.00802 -0.0709684
0.00804 -0.0709673
0.00806 -0.0709661
0.00808 -0.070965
0.0081 -0.0709639
0.00812 -0.0709628
0.00814 -0.0709617
0.00816 -0.0709606
0.00818 -0.0709596
0.0082 -0.0709585
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0.05994 -0.0708249

6. Method history of a simulation of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection with set duration and simulation time

Startup command : ./bin/ssp --cell cells/stand_alone.ndf --inject-magnitude 2e-8 --inject-delay 0.01 --inject-duration 0.03 --time 0.06 --output /stand_alone/segments/soma->Vm --history

Comments, Preparation, Reparation

1. Comment for this test definition
The --history option removes the time stamps from the output, making it less useful.
2. Preparation needed before the commands below : 
No preparation necessary
3. And repared afterwards using : 
Removing the output from the distribution, needed for distcheck to work properly

6.1. What is the method history when we run a schedule of a single neuron model from the cell builtin schedule, soma Vm output, soma current injection with set duration and simulation time ?

1. Expected output 

history:
  - arguments: []
    method: instantiate_services
  - arguments: []
    method: compile
  - arguments: []
    method: connect
  - arguments: []
    method: instantiate_inputs
  - arguments: []
    method: instantiate_outputs
  - arguments: []
    method: initiate
  - arguments: []
    method: optimize
  - arguments: []
    method: analyze
  - arguments:
      - 0.01
      - verbose: 0
    method: advance
  - arguments:
      - component_name: /stand_alone/segments/soma
        field: INJECT
        modelname: /stand_alone
        value: 2e-8
    method: apply_runtime_parameters
  - arguments:
      - 0.03
      - verbose: 0
    method: advance
  - arguments:
      - component_name: /stand_alone/segments/soma
        field: INJECT
        modelname: /stand_alone
        value: 0
    method: apply_runtime_parameters
  - arguments:
      - 0.02
      - verbose: 0
    method: advance
  - arguments: []
    method: finish

7. Simulation of a single neuron model from the cell builtin schedule, debug option turned on

This command definition is currently disabled (disabled is 'due to the context dependent name of the ssp executable, this test needs regexes to work properly, but that seems like to much work for the moment')

Startup command : ./bin/ssp --cell cells/stand_alone.ndf --debug 1 --verbose

Comments, Preparation, Reparation

1. Preparation needed before the commands below : 
No preparation necessary
2. And repared afterwards using : 
Removing the output from the distribution, needed for distcheck to work properly

7.1. Can we run a schedule of a single neuron model from the cell builtin schedule, debug option turned on ?

1. Expected output 
Inferring model name from cells/stand_alone.ndf, model name set to stand_alone
Use the --model-name option to overwrite
--- Running schedule
---
apply:
  simulation:
    - arguments:
        - 0.05
        - verbose: 0
      method: advance
models:
  - granular_parameters: []
    modelname: /stand_alone
    solverclass: heccer
name: 'builtin cell configuration, applied to: stand_alone'
outputclasses:
  double_2_ascii:
    module_name: Heccer
    options:
      filename: ./output/stand_alone.out
    package: Heccer::Output
outputs:
  - component_name: /stand_alone/segments/soma
    field: Vm
    outputclass: double_2_ascii
services:
  model_container:
    initializers:
      - arguments:
          -
            - ./bin/ssp
            - -P
            - cells/stand_alone.ndf
        method: read
    module_name: Neurospaces
solverclasses:
  heccer:
    module_name: Heccer
    service_name: model_container
usage: |2
  
  	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
  	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
  
          The name of the model neuron is inferred from the name of the model description file.
          (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
          called "hh_neuron").
  
  	--model-name overwrite the default model name.
  	--steps sets number of steps
---
1_DEBUG_subname: SSP::Debug::new
2_DEBUG_arguments:
  - SSP::Debug
  - apply:
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options:
          filename: ./output/stand_alone.out
        package: Heccer::Output
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    services:
      model_container:
        initializers:
          - arguments:
              -
                - ./bin/ssp
                - -P
                - cells/stand_alone.ndf
            method: read
        module_name: Neurospaces
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
---
1_DEBUG_subname: SSP::Debug::salvage
2_DEBUG_arguments:
  - !!perl/hash:SSP::Debug
    analyzers: {}
    apply:
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options:
          filename: ./output/stand_alone.out
        package: Heccer::Output
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    services:
      model_container:
        initializers:
          - arguments:
              -
                - ./bin/ssp
                - -P
                - cells/stand_alone.ndf
            method: read
        module_name: Neurospaces
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
./bin/ssp: Running schedule builtin cell configuration, applied to: stand_alone
---
1_DEBUG_subname: SSP::Debug::run
2_DEBUG_arguments:
  - !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default:
          - method: analyze
        priority: 95
      finishers:
        default:
          - method: finish
        priority: 140
      initializers:
        default:
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: []
        priority: 50
      results:
        default: []
        priority: 170
      services:
        default:
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options:
          filename: ./output/stand_alone.out
        package: Heccer::Output
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    services:
      model_container:
        initializers:
          - arguments:
              -
                - ./bin/ssp
                - -P
                - cells/stand_alone.ndf
            method: read
        model_library: /usr/local/neurospaces/models/library
        module_name: Neurospaces
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
---
1_DEBUG_subname: SSP::Debug::salvage
2_DEBUG_arguments:
  - !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default:
          - method: analyze
        priority: 95
      finishers:
        default:
          - method: finish
        priority: 140
      initializers:
        default:
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: []
        priority: 50
      results:
        default: []
        priority: 170
      services:
        default:
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options:
          filename: ./output/stand_alone.out
        package: Heccer::Output
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    services:
      model_container:
        initializers:
          - arguments:
              -
                - ./bin/ssp
                - -P
                - cells/stand_alone.ndf
            method: read
        model_library: /usr/local/neurospaces/models/library
        module_name: Neurospaces
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
./bin/ssp: applying method 'instantiate_services' to builtin cell configuration, applied to: stand_alone
---
1_DEBUG_subname: SSP::Debug::instantiate_services
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options:
          filename: ./output/stand_alone.out
        package: Heccer::Output
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    services:
      model_container:
        initializers:
          - arguments:
              -
                - ./bin/ssp
                - -P
                - cells/stand_alone.ndf
            method: read
        model_library: /usr/local/neurospaces/models/library
        module_name: Neurospaces
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
  - *1
./bin/ssp: applying method 'compile' to builtin cell configuration, applied to: stand_alone
---
1_DEBUG_subname: SSP::Debug::compile
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options:
          filename: ./output/stand_alone.out
        package: Heccer::Output
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    services:
      model_container:
        initializers: &8
          - arguments:
              -
                - ./bin/ssp
                - -P
                - cells/stand_alone.ndf
                - -m
                - /usr/local/neurospaces/models/library
            method: read
        model_library: /usr/local/neurospaces/models/library
        module_name: Neurospaces
        ssp_service: !!perl/hash:SSP::Service
          backend: !!perl/hash:Neurospaces
            initializers: *8
            model_library: /usr/local/neurospaces/models/library
            module_name: Neurospaces
            neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
          scheduler: *1
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
  - *1
./bin/ssp: applying method 'instantiate_inputs' to builtin cell configuration, applied to: stand_alone
---
1_DEBUG_subname: SSP::Debug::instantiate_inputs
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options:
          filename: ./output/stand_alone.out
        package: Heccer::Output
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    schedule:
      - !!perl/hash:SSP::Engine
        backend: !!perl/hash:Heccer
          event_distributor:
            event_distributor_backend: ~
            event_distributor_name: ~
          heccer: !!perl/hash:SwiggableHeccer::Heccer {}
          model_source:
            modelname: /stand_alone
            service_backend: &8 !!perl/hash:Neurospaces
              initializers: &9
                - arguments:
                    -
                      - ./bin/ssp
                      - -P
                      - cells/stand_alone.ndf
                      - -m
                      - /usr/local/neurospaces/models/library
                  method: read
              model_library: /usr/local/neurospaces/models/library
              module_name: Neurospaces
              neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
            service_name: model_container
        event_distributor: {}
        modelname: /stand_alone
        module_name: Heccer
        scheduler: *1
        service: &10
          initializers: *9
          model_library: /usr/local/neurospaces/models/library
          module_name: Neurospaces
          ssp_service: !!perl/hash:SSP::Service
            backend: *8
            scheduler: *1
        service_name: model_container
        solverclass: heccer
    services:
      model_container: *10
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      compile:
        - []
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
  - *1
./bin/ssp: applying method 'instantiate_outputs' to builtin cell configuration, applied to: stand_alone
---
1_DEBUG_subname: SSP::Debug::instantiate_outputs
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options:
          filename: ./output/stand_alone.out
        package: Heccer::Output
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    schedule:
      - !!perl/hash:SSP::Engine
        backend: !!perl/hash:Heccer
          event_distributor:
            event_distributor_backend: ~
            event_distributor_name: ~
          heccer: !!perl/hash:SwiggableHeccer::Heccer {}
          model_source:
            modelname: /stand_alone
            service_backend: &8 !!perl/hash:Neurospaces
              initializers: &9
                - arguments:
                    -
                      - ./bin/ssp
                      - -P
                      - cells/stand_alone.ndf
                      - -m
                      - /usr/local/neurospaces/models/library
                  method: read
              model_library: /usr/local/neurospaces/models/library
              module_name: Neurospaces
              neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
            service_name: model_container
        event_distributor: {}
        modelname: /stand_alone
        module_name: Heccer
        scheduler: *1
        service: &10
          initializers: *9
          model_library: /usr/local/neurospaces/models/library
          module_name: Neurospaces
          ssp_service: !!perl/hash:SSP::Service
            backend: *8
            scheduler: *1
        service_name: model_container
        solverclass: heccer
    services:
      model_container: *10
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      compile:
        - []
      instantiate_inputs:
        - []
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
  - *1
---
1_DEBUG_subname: SSP::Debug::lookup_solver_engine
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options: &8
          filename: ./output/stand_alone.out
        package: Heccer::Output
        ssp_outputclass: &9 !!perl/hash:SSP::Output
          backend: !!perl/hash:Heccer::Output
            backend: !!perl/hash:SwiggableHeccer::OutputGenerator {}
            filename: ./output/stand_alone.out
            module_name: Heccer
            name: double_2_ascii
            options: *8
            package: Heccer::Output
            scheduler: *1
          module_name: Heccer
          name: double_2_ascii
          options: *8
          package: Heccer::Output
          scheduler: *1
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    schedule:
      - !!perl/hash:SSP::Engine
        backend: !!perl/hash:Heccer
          event_distributor:
            event_distributor_backend: ~
            event_distributor_name: ~
          heccer: !!perl/hash:SwiggableHeccer::Heccer {}
          model_source:
            modelname: /stand_alone
            service_backend: &10 !!perl/hash:Neurospaces
              initializers: &11
                - arguments:
                    -
                      - ./bin/ssp
                      - -P
                      - cells/stand_alone.ndf
                      - -m
                      - /usr/local/neurospaces/models/library
                  method: read
              model_library: /usr/local/neurospaces/models/library
              module_name: Neurospaces
              neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
            service_name: model_container
        event_distributor: {}
        modelname: /stand_alone
        module_name: Heccer
        scheduler: *1
        service: &12
          initializers: *11
          model_library: /usr/local/neurospaces/models/library
          module_name: Neurospaces
          ssp_service: !!perl/hash:SSP::Service
            backend: *10
            scheduler: *1
        service_name: model_container
        solverclass: heccer
      - *9
    services:
      neurospaces: *12
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      compile:
        - []
      instantiate_inputs:
        - []
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
  - model_container::/stand_alone
./bin/ssp: applying method 'initiate' to builtin cell configuration, applied to: stand_alone
---
1_DEBUG_subname: SSP::Debug::initiate
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options: &8
          filename: ./output/stand_alone.out
        package: Heccer::Output
        ssp_outputclass: &9 !!perl/hash:SSP::Output
          backend: !!perl/hash:Heccer::Output
            backend: !!perl/hash:SwiggableHeccer::OutputGenerator {}
            filename: ./output/stand_alone.out
            module_name: Heccer
            name: double_2_ascii
            options: *8
            package: Heccer::Output
            scheduler: *1
          module_name: Heccer
          name: double_2_ascii
          options: *8
          package: Heccer::Output
          scheduler: *1
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    schedule:
      - !!perl/hash:SSP::Engine
        backend: !!perl/hash:Heccer
          event_distributor:
            event_distributor_backend: ~
            event_distributor_name: ~
          heccer: !!perl/hash:SwiggableHeccer::Heccer {}
          model_source:
            modelname: /stand_alone
            service_backend: &10 !!perl/hash:Neurospaces
              initializers: &11
                - arguments:
                    -
                      - ./bin/ssp
                      - -P
                      - cells/stand_alone.ndf
                      - -m
                      - /usr/local/neurospaces/models/library
                  method: read
              model_library: /usr/local/neurospaces/models/library
              module_name: Neurospaces
              neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
            service_name: model_container
        event_distributor: {}
        modelname: /stand_alone
        module_name: Heccer
        scheduler: *1
        service: &12
          initializers: *11
          model_library: /usr/local/neurospaces/models/library
          module_name: Neurospaces
          ssp_service: !!perl/hash:SSP::Service
            backend: *10
            scheduler: *1
        service_name: model_container
        solverclass: heccer
      - *9
    services:
      neurospaces: *12
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      compile:
        - []
      instantiate_inputs:
        - []
      instantiate_outputs:
        - []
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
  - *1
./bin/ssp: applying method 'analyze' to builtin cell configuration, applied to: stand_alone
---
1_DEBUG_subname: SSP::Debug::analyze
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options: &8
          filename: ./output/stand_alone.out
        package: Heccer::Output
        ssp_outputclass: &9 !!perl/hash:SSP::Output
          backend: !!perl/hash:Heccer::Output
            backend: !!perl/hash:SwiggableHeccer::OutputGenerator {}
            filename: ./output/stand_alone.out
            module_name: Heccer
            name: double_2_ascii
            options: *8
            package: Heccer::Output
            scheduler: *1
          module_name: Heccer
          name: double_2_ascii
          options: *8
          package: Heccer::Output
          scheduler: *1
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    schedule:
      - !!perl/hash:SSP::Engine
        backend: !!perl/hash:Heccer
          event_distributor:
            event_distributor_backend: ~
            event_distributor_name: ~
          heccer: !!perl/hash:SwiggableHeccer::Heccer {}
          model_source:
            modelname: /stand_alone
            service_backend: &10 !!perl/hash:Neurospaces
              initializers: &11
                - arguments:
                    -
                      - ./bin/ssp
                      - -P
                      - cells/stand_alone.ndf
                      - -m
                      - /usr/local/neurospaces/models/library
                  method: read
              model_library: /usr/local/neurospaces/models/library
              module_name: Neurospaces
              neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
            service_name: model_container
        event_distributor: {}
        modelname: /stand_alone
        module_name: Heccer
        scheduler: *1
        service: &12
          initializers: *11
          model_library: /usr/local/neurospaces/models/library
          module_name: Neurospaces
          ssp_service: !!perl/hash:SSP::Service
            backend: *10
            scheduler: *1
        service_name: model_container
        solverclass: heccer
      - *9
    services:
      model_container: *12
    simulation_time:
      steps: 0
      time: 0
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      compile:
        - []
      initiate:
        - []
      instantiate_inputs:
        - []
      instantiate_outputs:
        - []
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
  - *1
./bin/ssp: applying method 'advance' to builtin cell configuration, applied to: stand_alone
---
1_DEBUG_subname: SSP::Debug::advance
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments:
            - 0.05
            - &8
              verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options: &9
          filename: ./output/stand_alone.out
        package: Heccer::Output
        ssp_outputclass: &10 !!perl/hash:SSP::Output
          backend: !!perl/hash:Heccer::Output
            backend: !!perl/hash:SwiggableHeccer::OutputGenerator {}
            filename: ./output/stand_alone.out
            module_name: Heccer
            name: double_2_ascii
            options: *9
            package: Heccer::Output
            scheduler: *1
          module_name: Heccer
          name: double_2_ascii
          options: *9
          package: Heccer::Output
          scheduler: *1
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    schedule:
      - !!perl/hash:SSP::Engine
        backend: !!perl/hash:Heccer
          event_distributor:
            event_distributor_backend: ~
            event_distributor_name: ~
          heccer: !!perl/hash:SwiggableHeccer::Heccer {}
          model_source:
            modelname: /stand_alone
            service_backend: &11 !!perl/hash:Neurospaces
              initializers: &12
                - arguments:
                    -
                      - ./bin/ssp
                      - -P
                      - cells/stand_alone.ndf
                      - -m
                      - /usr/local/neurospaces/models/library
                  method: read
              model_library: /usr/local/neurospaces/models/library
              module_name: Neurospaces
              neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
            service_name: model_container
        event_distributor: {}
        modelname: /stand_alone
        module_name: Heccer
        scheduler: *1
        service: &13
          initializers: *12
          model_library: /usr/local/neurospaces/models/library
          module_name: Neurospaces
          ssp_service: !!perl/hash:SSP::Service
            backend: *11
            scheduler: *1
        service_name: model_container
        solverclass: heccer
      - *10
    services:
      model_container: *13
    simulation_time:
      steps: 0
      time: 0
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      analyze:
        - []
      compile:
        - []
      initiate:
        - []
      instantiate_inputs:
        - []
      instantiate_outputs:
        - []
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
  - *1
  - 0.05
  - *8
---
1_DEBUG_subname: SSP::Debug::get_time_step
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options: &8
          filename: ./output/stand_alone.out
        package: Heccer::Output
        ssp_outputclass: &9 !!perl/hash:SSP::Output
          backend: !!perl/hash:Heccer::Output
            backend: !!perl/hash:SwiggableHeccer::OutputGenerator {}
            filename: ./output/stand_alone.out
            module_name: Heccer
            name: double_2_ascii
            options: *8
            package: Heccer::Output
            scheduler: *1
          module_name: Heccer
          name: double_2_ascii
          options: *8
          package: Heccer::Output
          scheduler: *1
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    schedule:
      - !!perl/hash:SSP::Engine
        backend: !!perl/hash:Heccer
          event_distributor:
            event_distributor_backend: ~
            event_distributor_name: ~
          heccer: !!perl/hash:SwiggableHeccer::Heccer {}
          model_source:
            modelname: /stand_alone
            service_backend: &10 !!perl/hash:Neurospaces
              initializers: &11
                - arguments:
                    -
                      - ./bin/ssp
                      - -P
                      - cells/stand_alone.ndf
                      - -m
                      - /usr/local/neurospaces/models/library
                  method: read
              model_library: /usr/local/neurospaces/models/library
              module_name: Neurospaces
              neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
            service_name: model_container
        event_distributor: {}
        modelname: /stand_alone
        module_name: Heccer
        scheduler: *1
        service: &12
          initializers: *11
          model_library: /usr/local/neurospaces/models/library
          module_name: Neurospaces
          ssp_service: !!perl/hash:SSP::Service
            backend: *10
            scheduler: *1
        service_name: model_container
        solverclass: heccer
      - *9
    services:
      model_container: *12
    simulation_time:
      steps: 0
      time: 0
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      analyze:
        - []
      compile:
        - []
      initiate:
        - []
      instantiate_inputs:
        - []
      instantiate_outputs:
        - []
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
---
1_DEBUG_subname: SSP::Debug::steps
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments:
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options: &8
          filename: ./output/stand_alone.out
        package: Heccer::Output
        ssp_outputclass: &9 !!perl/hash:SSP::Output
          backend: !!perl/hash:Heccer::Output
            backend: !!perl/hash:SwiggableHeccer::OutputGenerator {}
            filename: ./output/stand_alone.out
            module_name: Heccer
            name: double_2_ascii
            options: *8
            package: Heccer::Output
            scheduler: *1
          module_name: Heccer
          name: double_2_ascii
          options: *8
          package: Heccer::Output
          scheduler: *1
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    schedule:
      - !!perl/hash:SSP::Engine
        backend: !!perl/hash:Heccer
          event_distributor:
            event_distributor_backend: ~
            event_distributor_name: ~
          heccer: !!perl/hash:SwiggableHeccer::Heccer {}
          model_source:
            modelname: /stand_alone
            service_backend: &10 !!perl/hash:Neurospaces
              initializers: &11
                - arguments:
                    -
                      - ./bin/ssp
                      - -P
                      - cells/stand_alone.ndf
                      - -m
                      - /usr/local/neurospaces/models/library
                  method: read
              model_library: /usr/local/neurospaces/models/library
              module_name: Neurospaces
              neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
            service_name: model_container
        event_distributor: {}
        modelname: /stand_alone
        module_name: Heccer
        scheduler: *1
        service: &12
          initializers: *11
          model_library: /usr/local/neurospaces/models/library
          module_name: Neurospaces
          ssp_service: !!perl/hash:SSP::Service
            backend: *10
            scheduler: *1
        service_name: model_container
        solverclass: heccer
      - *9
    services:
      model_container: *12
    simulation_time:
      steps: 0
      time: 0
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      analyze:
        - []
      compile:
        - []
      initiate:
        - []
      instantiate_inputs:
        - []
      instantiate_outputs:
        - []
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
  - *1
  - 2500
./bin/ssp: applying method 'finish' to builtin cell configuration, applied to: stand_alone
---
1_DEBUG_subname: SSP::Debug::finish
2_DEBUG_arguments:
  - &1 !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &2
          - method: analyze
        priority: 95
      finishers:
        default: &3
          - method: finish
        priority: 140
      initializers:
        default: &4
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &5 []
        priority: 50
      results:
        default: &6 []
        priority: 170
      services:
        default: &7
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *2
      finishers: *3
      initializers: *4
      modifiers: *5
      results: *6
      services: *7
      simulation:
        - arguments: &8
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options: &9
          filename: ./output/stand_alone.out
        package: Heccer::Output
        ssp_outputclass: &10 !!perl/hash:SSP::Output
          backend: !!perl/hash:Heccer::Output
            backend: !!perl/hash:SwiggableHeccer::OutputGenerator {}
            filename: ./output/stand_alone.out
            module_name: Heccer
            name: double_2_ascii
            options: *9
            package: Heccer::Output
            scheduler: *1
          module_name: Heccer
          name: double_2_ascii
          options: *9
          package: Heccer::Output
          scheduler: *1
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    schedule:
      - !!perl/hash:SSP::Engine
        backend: !!perl/hash:Heccer
          event_distributor:
            event_distributor_backend: ~
            event_distributor_name: ~
          heccer: !!perl/hash:SwiggableHeccer::Heccer {}
          model_source:
            modelname: /stand_alone
            service_backend: &11 !!perl/hash:Neurospaces
              initializers: &12
                - arguments:
                    -
                      - ./bin/ssp
                      - -P
                      - cells/stand_alone.ndf
                      - -m
                      - /usr/local/neurospaces/models/library
                  method: read
              model_library: /usr/local/neurospaces/models/library
              module_name: Neurospaces
              neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
            service_name: model_container
        event_distributor: {}
        modelname: /stand_alone
        module_name: Heccer
        scheduler: *1
        service: &13
          initializers: *12
          model_library: /usr/local/neurospaces/models/library
          module_name: Neurospaces
          ssp_service: !!perl/hash:SSP::Service
            backend: *11
            scheduler: *1
        service_name: model_container
        solverclass: heccer
      - *10
    services:
      model_container: *13
    simulation_time:
      steps: 2500
      time: ~
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      advance:
        - *8
      analyze:
        - []
      compile:
        - []
      initiate:
        - []
      instantiate_inputs:
        - []
      instantiate_outputs:
        - []
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
  - *1

output files follow
---
---
1_DEBUG_subname: SSP::Debug::DESTROY
2_DEBUG_arguments:
  - !!perl/hash:SSP::Debug
    analyzers: {}
    application_classes:
      analyzers:
        default: &1
          - method: analyze
        priority: 95
      finishers:
        default: &2
          - method: finish
        priority: 140
      initializers:
        default: &3
          - method: compile
          - method: instantiate_inputs
          - method: instantiate_outputs
          - method: initiate
        priority: 80
      modifiers:
        default: &4 []
        priority: 50
      results:
        default: &5 []
        priority: 170
      services:
        default: &6
          - method: instantiate_services
        priority: 20
      simulation:
        default: []
        priority: 110
    apply:
      analyzers: *1
      finishers: *2
      initializers: *3
      modifiers: *4
      results: *5
      services: *6
      simulation:
        - arguments: &7
            - 0.05
            - verbose: 0
          method: advance
    models:
      - granular_parameters: []
        modelname: /stand_alone
        solverclass: heccer
    name: 'builtin cell configuration, applied to: stand_alone'
    outputclasses:
      double_2_ascii:
        module_name: Heccer
        options:
          filename: ./output/stand_alone.out
        package: Heccer::Output
        ssp_outputclass: ~
    outputs:
      - component_name: /stand_alone/segments/soma
        field: Vm
        outputclass: double_2_ascii
    schedule:
      - ~
      - ~
    services:
      model_container:
        initializers:
          - arguments:
              -
                - ./bin/ssp
                - -P
                - cells/stand_alone.ndf
                - -m
                - /usr/local/neurospaces/models/library
            method: read
        model_library: /usr/local/neurospaces/models/library
        module_name: Neurospaces
        ssp_service: !!perl/hash:SSP::Service
          backend: ~
          scheduler: ~
    simulation_time:
      steps: 2500
      time: ~
    solverclasses:
      heccer:
        module_name: Heccer
        service_name: model_container
    status:
      advance:
        - *7
      analyze:
        - []
      compile:
        - []
      finish:
        - []
      initiate:
        - []
      instantiate_inputs:
        - []
      instantiate_outputs:
        - []
      instantiate_services:
        - []
    usage: |2
      
      	Simulate a single model neuron, default is to output the membrane potential of the soma.
  	Use the options to inject current in the soma (--inject-magnitude), or alternatively
  	to set a command voltage (--perfectclamp).
      	The model's soma segment must reside in a SEGMENT_GROUP with name "segments".
      
              The name of the model neuron is inferred from the name of the model description file.
              (e.g. a model description file called "hh_neuron.ndf" is assumed to define a model neuron
              called "hh_neuron").
      
      	--model-name overwrite the default model name.
      	--steps sets number of steps
    verbose: 1
undefined_method SSP::DESTROY
2. This test is currently not executed
(disabled is 'due to the context dependent name of the ssp executable, this test needs regexes to work properly, but that seems like to much work for the moment')

8. Invocation of the neurospaces studio when using the cell builtin

This command definition is currently disabled (disabled is 'cannot load the neurospaces studio')

Startup command : ./bin/ssp --cell examples/hh_neuron.ndf --time 0.5 --inject-magnitude 2e-8 --neurospaces-studio --emit-schedule

8.1. Can we invoke the neurospaces studio when using the cell builtin ?

1. Expected output 
apply:
  initializers:
    - ~
  simulation:
    - arguments:
        - (.*?)/bin/ssp
      method: Neurospaces::GUI::gui
models:
  - granular_parameters:
      - component_name: /hh_neuron/segments/soma
        field: INJECT
        value: 2e-8
        warn_only: 'the component_name is a default, its address may be wrong'
      - component_name: /hh_neuron/soma
        field: INJECT
        value: 2e-8
        warn_only: 'the component_name is a default, its address may be wrong'
    modelname: /hh_neuron
    solverclass: heccer
name: 'builtin cell configuration, applied to: hh_neuron'
outputclasses:
  double_2_ascii:
    module_name: Heccer
    options:
      filename: \./output/hh_neuron\.out
    package: Heccer::Output
outputs:
  - component_name: /hh_neuron/segments/soma
    field: Vm
    outputclass: double_2_ascii
services:
  model_container:
    initializers:
      - arguments:
          -
            - (.*?)/bin/ssp
            - -P
            - examples/hh_neuron\.ndf
        method: read
    model_library: /usr/local/neurospaces/models/library
    module_name: Neurospaces
solverclasses:
  heccer:
    module_name: Heccer
    service_name: model_container
2. This test is currently not executed
(disabled is 'cannot load the neurospaces studio')